P2 GEO GTEx and combination.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Requiremnts\n",
    "import os\n",
    "import shutil\n",
    "import tempfile\n",
    "import glob\n",
    "import re\n",
    "import matplotlib\n",
    "import numpy\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import pandas as pd"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tidy data (preprocessing raw data before integration)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE184951_RAW"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "c:\\Users\\Hua\\Desktop\\Omics\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "['c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602348_Control-1.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602349_Control-12.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602350_Control-13.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602351_Control-2.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602352_Control-3.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602353_Control-4.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602354_Control-6.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602355_Control-7.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602356_Control-8.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602357_Control-9.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602358_Post-S1.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602359_Post-S12.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602360_Post-S13.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602361_Post-S2.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602362_Post-S3.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602363_Post-S4.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602364_Post-S5.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602365_Post-S6.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602366_Post-S7.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602367_Post-S8.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602368_Post-S9.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602369_Pre-S1.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602370_Pre-S12.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602371_Pre-S13.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602372_Pre-S2.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602373_Pre-S3.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602374_Pre-S4.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602375_Pre-S5.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602376_Pre-S6.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602377_Pre-S7.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602378_Pre-S8.geneCounts.txt',\n",
       " 'c:\\\\Users\\\\Hua\\\\Desktop\\\\Omics\\\\GEO_data\\\\GSE184951_RAW\\\\GSM5602379_Pre-S9.geneCounts.txt']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Setup data directory\n",
    "directory = os.environ.get(\"GEO_data/GSE184951_RAW\")\n",
    "root_dir = os.getcwd() if directory is None else directory\n",
    "print(root_dir)\n",
    "\n",
    "# set Rawdata_dicts\n",
    "Sample_series = sorted(\n",
    "    glob.glob(os.path.join(root_dir,  \"GEO_data\", \"GSE184951_RAW\", \"*.txt\")))\n",
    "\n",
    "\n",
    "Sample_series"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Control-12'"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "patient_name = re.search(\"(?<=(GSM5602....)).+\\d(?=\\.)\", Sample_series[1]).group(0)\n",
    "patient_name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "Annotation_dict = pd.read_table(Sample_series[1], names=['GeneID', 'GeneSymbol', 'Count'], header=None)[0:63676][['GeneID', 'GeneSymbol']]\n",
    "\n",
    "Annotation_dict.to_csv('Annotation_dict.csv', encoding='utf_8_sig', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Control-1',\n",
       " 'Control-12',\n",
       " 'Control-13',\n",
       " 'Control-2',\n",
       " 'Control-3',\n",
       " 'Control-4',\n",
       " 'Control-6',\n",
       " 'Control-7',\n",
       " 'Control-8',\n",
       " 'Control-9',\n",
       " 'Post-S1',\n",
       " 'Post-S12',\n",
       " 'Post-S13',\n",
       " 'Post-S2',\n",
       " 'Post-S3',\n",
       " 'Post-S4',\n",
       " 'Post-S5',\n",
       " 'Post-S6',\n",
       " 'Post-S7',\n",
       " 'Post-S8',\n",
       " 'Post-S9',\n",
       " 'Pre-S1',\n",
       " 'Pre-S12',\n",
       " 'Pre-S13',\n",
       " 'Pre-S2',\n",
       " 'Pre-S3',\n",
       " 'Pre-S4',\n",
       " 'Pre-S5',\n",
       " 'Pre-S6',\n",
       " 'Pre-S7',\n",
       " 'Pre-S8',\n",
       " 'Pre-S9']"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Control-1</th>\n",
       "      <th>Control-12</th>\n",
       "      <th>Control-13</th>\n",
       "      <th>Control-2</th>\n",
       "      <th>Control-3</th>\n",
       "      <th>Control-4</th>\n",
       "      <th>Control-6</th>\n",
       "      <th>Control-7</th>\n",
       "      <th>Control-8</th>\n",
       "      <th>Control-9</th>\n",
       "      <th>...</th>\n",
       "      <th>Pre-S12</th>\n",
       "      <th>Pre-S13</th>\n",
       "      <th>Pre-S2</th>\n",
       "      <th>Pre-S3</th>\n",
       "      <th>Pre-S4</th>\n",
       "      <th>Pre-S5</th>\n",
       "      <th>Pre-S6</th>\n",
       "      <th>Pre-S7</th>\n",
       "      <th>Pre-S8</th>\n",
       "      <th>Pre-S9</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>104</td>\n",
       "      <td>127</td>\n",
       "      <td>161</td>\n",
       "      <td>140</td>\n",
       "      <td>133</td>\n",
       "      <td>83</td>\n",
       "      <td>123</td>\n",
       "      <td>104</td>\n",
       "      <td>80</td>\n",
       "      <td>94</td>\n",
       "      <td>...</td>\n",
       "      <td>137</td>\n",
       "      <td>102</td>\n",
       "      <td>136</td>\n",
       "      <td>115</td>\n",
       "      <td>104</td>\n",
       "      <td>111</td>\n",
       "      <td>205</td>\n",
       "      <td>134</td>\n",
       "      <td>92</td>\n",
       "      <td>206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>9</td>\n",
       "      <td>17</td>\n",
       "      <td>679</td>\n",
       "      <td>16</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>21</td>\n",
       "      <td>16</td>\n",
       "      <td>17</td>\n",
       "      <td>13</td>\n",
       "      <td>...</td>\n",
       "      <td>14</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "      <td>9</td>\n",
       "      <td>33</td>\n",
       "      <td>2</td>\n",
       "      <td>275</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>93</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1609</td>\n",
       "      <td>1785</td>\n",
       "      <td>1542</td>\n",
       "      <td>1876</td>\n",
       "      <td>1398</td>\n",
       "      <td>2057</td>\n",
       "      <td>2433</td>\n",
       "      <td>1642</td>\n",
       "      <td>1614</td>\n",
       "      <td>1635</td>\n",
       "      <td>...</td>\n",
       "      <td>759</td>\n",
       "      <td>842</td>\n",
       "      <td>530</td>\n",
       "      <td>714</td>\n",
       "      <td>658</td>\n",
       "      <td>709</td>\n",
       "      <td>562</td>\n",
       "      <td>881</td>\n",
       "      <td>801</td>\n",
       "      <td>880</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>453</td>\n",
       "      <td>507</td>\n",
       "      <td>467</td>\n",
       "      <td>440</td>\n",
       "      <td>545</td>\n",
       "      <td>396</td>\n",
       "      <td>438</td>\n",
       "      <td>475</td>\n",
       "      <td>304</td>\n",
       "      <td>485</td>\n",
       "      <td>...</td>\n",
       "      <td>361</td>\n",
       "      <td>303</td>\n",
       "      <td>247</td>\n",
       "      <td>280</td>\n",
       "      <td>260</td>\n",
       "      <td>296</td>\n",
       "      <td>282</td>\n",
       "      <td>323</td>\n",
       "      <td>274</td>\n",
       "      <td>249</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>122</td>\n",
       "      <td>128</td>\n",
       "      <td>161</td>\n",
       "      <td>140</td>\n",
       "      <td>138</td>\n",
       "      <td>94</td>\n",
       "      <td>108</td>\n",
       "      <td>152</td>\n",
       "      <td>49</td>\n",
       "      <td>176</td>\n",
       "      <td>...</td>\n",
       "      <td>90</td>\n",
       "      <td>88</td>\n",
       "      <td>93</td>\n",
       "      <td>74</td>\n",
       "      <td>68</td>\n",
       "      <td>87</td>\n",
       "      <td>99</td>\n",
       "      <td>94</td>\n",
       "      <td>53</td>\n",
       "      <td>101</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63671</th>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>20</td>\n",
       "      <td>9</td>\n",
       "      <td>6</td>\n",
       "      <td>9</td>\n",
       "      <td>22</td>\n",
       "      <td>25</td>\n",
       "      <td>10</td>\n",
       "      <td>11</td>\n",
       "      <td>...</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>14</td>\n",
       "      <td>11</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63672</th>\n",
       "      <td>19</td>\n",
       "      <td>6</td>\n",
       "      <td>20</td>\n",
       "      <td>48</td>\n",
       "      <td>22</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>23</td>\n",
       "      <td>6</td>\n",
       "      <td>16</td>\n",
       "      <td>...</td>\n",
       "      <td>12</td>\n",
       "      <td>18</td>\n",
       "      <td>10</td>\n",
       "      <td>12</td>\n",
       "      <td>5</td>\n",
       "      <td>10</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63673</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63674</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63675</th>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>63676 rows × 32 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Control-1  Control-12  Control-13  Control-2  Control-3  Control-4  \\\n",
       "0            104         127         161        140        133         83   \n",
       "1              9          17         679         16          6          3   \n",
       "2           1609        1785        1542       1876       1398       2057   \n",
       "3            453         507         467        440        545        396   \n",
       "4            122         128         161        140        138         94   \n",
       "...          ...         ...         ...        ...        ...        ...   \n",
       "63671         12          12          20          9          6          9   \n",
       "63672         19           6          20         48         22          8   \n",
       "63673          0           0           0          0          0          0   \n",
       "63674          0           0           0          0          0          0   \n",
       "63675          2           3           2          3          0          0   \n",
       "\n",
       "       Control-6  Control-7  Control-8  Control-9  ...  Pre-S12  Pre-S13  \\\n",
       "0            123        104         80         94  ...      137      102   \n",
       "1             21         16         17         13  ...       14       23   \n",
       "2           2433       1642       1614       1635  ...      759      842   \n",
       "3            438        475        304        485  ...      361      303   \n",
       "4            108        152         49        176  ...       90       88   \n",
       "...          ...        ...        ...        ...  ...      ...      ...   \n",
       "63671         22         25         10         11  ...        9        8   \n",
       "63672          8         23          6         16  ...       12       18   \n",
       "63673          0          0          0          0  ...        0        0   \n",
       "63674          0          0          0          0  ...        0        0   \n",
       "63675          0          1          0          0  ...        0        0   \n",
       "\n",
       "       Pre-S2  Pre-S3  Pre-S4  Pre-S5  Pre-S6  Pre-S7  Pre-S8  Pre-S9  \n",
       "0         136     115     104     111     205     134      92     206  \n",
       "1          22       9      33       2     275       4       5      93  \n",
       "2         530     714     658     709     562     881     801     880  \n",
       "3         247     280     260     296     282     323     274     249  \n",
       "4          93      74      68      87      99      94      53     101  \n",
       "...       ...     ...     ...     ...     ...     ...     ...     ...  \n",
       "63671       7       6      14      11       4       4       5      10  \n",
       "63672      10      12       5      10       2       5       6       7  \n",
       "63673       0       0       0       0       0       0       0       0  \n",
       "63674       0       0       0       0       0       0       0       0  \n",
       "63675       1       4       0       1       0       0       1       0  \n",
       "\n",
       "[63676 rows x 32 columns]"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Names = []\n",
    "Counts = []\n",
    "\n",
    "for a in Sample_series:\n",
    "    Count_one = pd.read_table(a, names=['GeneID', 'GeneSymbol', 'Count'], header=None)[0:63676].Count\n",
    "    Name_one = re.search(\"(?<=(GSM5602....)).+\\d(?=\\.)\", a).group(0)\n",
    "    Names.append(Name_one)\n",
    "    Counts.append(Count_one)\n",
    "\n",
    "Count_table = pd.DataFrame(dict(zip(Names, Counts)))\n",
    "Count_table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.concat([Annotation_dict,Count_table], axis=1).to_csv('GSE184951_rawcount.csv', encoding='utf_8_sig', index=False)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GTEx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>GeneSymbol</th>\n",
       "      <th>GTEX-1117F-0426-SM-5EGHI</th>\n",
       "      <th>GTEX-111CU-2026-SM-5GZZC</th>\n",
       "      <th>GTEX-111FC-0326-SM-5GZZ1</th>\n",
       "      <th>GTEX-111VG-2626-SM-5GZY2</th>\n",
       "      <th>GTEX-111YS-2326-SM-5987L</th>\n",
       "      <th>GTEX-1122O-2426-SM-5GIDN</th>\n",
       "      <th>GTEX-1128S-2426-SM-5H11B</th>\n",
       "      <th>GTEX-113JC-2726-SM-5EGIS</th>\n",
       "      <th>...</th>\n",
       "      <th>GTEX-ZY6K-2026-SM-5GZXQ</th>\n",
       "      <th>GTEX-ZYFC-0526-SM-5GIDF</th>\n",
       "      <th>GTEX-ZYFD-0326-SM-5NQ8I</th>\n",
       "      <th>GTEX-ZYFG-2426-SM-5GIE8</th>\n",
       "      <th>GTEX-ZYT6-1626-SM-5E45R</th>\n",
       "      <th>GTEX-ZYW4-0526-SM-5GZZ5</th>\n",
       "      <th>GTEX-ZYY3-0526-SM-5E45G</th>\n",
       "      <th>GTEX-ZZ64-1526-SM-5E43K</th>\n",
       "      <th>GTEX-ZZPT-0626-SM-5GZXT</th>\n",
       "      <th>GTEX-ZZPU-2626-SM-5E45Y</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000223972.5</td>\n",
       "      <td>DDX11L1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000227232.5</td>\n",
       "      <td>WASH7P</td>\n",
       "      <td>109</td>\n",
       "      <td>40</td>\n",
       "      <td>52</td>\n",
       "      <td>19</td>\n",
       "      <td>29</td>\n",
       "      <td>64</td>\n",
       "      <td>66</td>\n",
       "      <td>33</td>\n",
       "      <td>...</td>\n",
       "      <td>223</td>\n",
       "      <td>69</td>\n",
       "      <td>32</td>\n",
       "      <td>47</td>\n",
       "      <td>27</td>\n",
       "      <td>44</td>\n",
       "      <td>65</td>\n",
       "      <td>74</td>\n",
       "      <td>99</td>\n",
       "      <td>34</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267.1</td>\n",
       "      <td>MIR6859-1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485.5</td>\n",
       "      <td>MIR1302-2HG</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000237613.2</td>\n",
       "      <td>FAM138A</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56195</th>\n",
       "      <td>ENSG00000198695.2</td>\n",
       "      <td>MT-ND6</td>\n",
       "      <td>164596</td>\n",
       "      <td>271981</td>\n",
       "      <td>104807</td>\n",
       "      <td>153177</td>\n",
       "      <td>185456</td>\n",
       "      <td>199394</td>\n",
       "      <td>445293</td>\n",
       "      <td>129277</td>\n",
       "      <td>...</td>\n",
       "      <td>151860</td>\n",
       "      <td>204304</td>\n",
       "      <td>108419</td>\n",
       "      <td>365195</td>\n",
       "      <td>133850</td>\n",
       "      <td>247638</td>\n",
       "      <td>119170</td>\n",
       "      <td>294986</td>\n",
       "      <td>37886</td>\n",
       "      <td>303816</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56196</th>\n",
       "      <td>ENSG00000210194.1</td>\n",
       "      <td>MT-TE</td>\n",
       "      <td>65</td>\n",
       "      <td>120</td>\n",
       "      <td>41</td>\n",
       "      <td>67</td>\n",
       "      <td>85</td>\n",
       "      <td>86</td>\n",
       "      <td>139</td>\n",
       "      <td>46</td>\n",
       "      <td>...</td>\n",
       "      <td>49</td>\n",
       "      <td>90</td>\n",
       "      <td>35</td>\n",
       "      <td>189</td>\n",
       "      <td>17</td>\n",
       "      <td>102</td>\n",
       "      <td>45</td>\n",
       "      <td>151</td>\n",
       "      <td>8</td>\n",
       "      <td>120</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56197</th>\n",
       "      <td>ENSG00000198727.2</td>\n",
       "      <td>MT-CYB</td>\n",
       "      <td>638209</td>\n",
       "      <td>1114514</td>\n",
       "      <td>1318175</td>\n",
       "      <td>650782</td>\n",
       "      <td>922519</td>\n",
       "      <td>921817</td>\n",
       "      <td>1814597</td>\n",
       "      <td>900959</td>\n",
       "      <td>...</td>\n",
       "      <td>1304160</td>\n",
       "      <td>814191</td>\n",
       "      <td>902797</td>\n",
       "      <td>1181827</td>\n",
       "      <td>1237537</td>\n",
       "      <td>644574</td>\n",
       "      <td>1027530</td>\n",
       "      <td>1084657</td>\n",
       "      <td>680051</td>\n",
       "      <td>1231647</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56198</th>\n",
       "      <td>ENSG00000210195.2</td>\n",
       "      <td>MT-TT</td>\n",
       "      <td>9</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>224</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>93</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56199</th>\n",
       "      <td>ENSG00000210196.2</td>\n",
       "      <td>MT-TP</td>\n",
       "      <td>9</td>\n",
       "      <td>4</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>5</td>\n",
       "      <td>3</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>57</td>\n",
       "      <td>276</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>56200 rows × 805 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  GeneID   GeneSymbol  GTEX-1117F-0426-SM-5EGHI  \\\n",
       "0      ENSG00000223972.5      DDX11L1                         0   \n",
       "1      ENSG00000227232.5       WASH7P                       109   \n",
       "2      ENSG00000278267.1    MIR6859-1                         0   \n",
       "3      ENSG00000243485.5  MIR1302-2HG                         0   \n",
       "4      ENSG00000237613.2      FAM138A                         0   \n",
       "...                  ...          ...                       ...   \n",
       "56195  ENSG00000198695.2       MT-ND6                    164596   \n",
       "56196  ENSG00000210194.1        MT-TE                        65   \n",
       "56197  ENSG00000198727.2       MT-CYB                    638209   \n",
       "56198  ENSG00000210195.2        MT-TT                         9   \n",
       "56199  ENSG00000210196.2        MT-TP                         9   \n",
       "\n",
       "       GTEX-111CU-2026-SM-5GZZC  GTEX-111FC-0326-SM-5GZZ1  \\\n",
       "0                             0                         1   \n",
       "1                            40                        52   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             0                         1   \n",
       "...                         ...                       ...   \n",
       "56195                    271981                    104807   \n",
       "56196                       120                        41   \n",
       "56197                   1114514                   1318175   \n",
       "56198                         2                         4   \n",
       "56199                         4                         6   \n",
       "\n",
       "       GTEX-111VG-2626-SM-5GZY2  GTEX-111YS-2326-SM-5987L  \\\n",
       "0                             0                         0   \n",
       "1                            19                        29   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             1                         2   \n",
       "...                         ...                       ...   \n",
       "56195                    153177                    185456   \n",
       "56196                        67                        85   \n",
       "56197                    650782                    922519   \n",
       "56198                         1                         4   \n",
       "56199                         2                         4   \n",
       "\n",
       "       GTEX-1122O-2426-SM-5GIDN  GTEX-1128S-2426-SM-5H11B  \\\n",
       "0                             0                         0   \n",
       "1                            64                        66   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             1                         0   \n",
       "...                         ...                       ...   \n",
       "56195                    199394                    445293   \n",
       "56196                        86                       139   \n",
       "56197                    921817                   1814597   \n",
       "56198                         1                         7   \n",
       "56199                         3                         5   \n",
       "\n",
       "       GTEX-113JC-2726-SM-5EGIS  ...  GTEX-ZY6K-2026-SM-5GZXQ  \\\n",
       "0                             0  ...                        3   \n",
       "1                            33  ...                      223   \n",
       "2                             0  ...                        0   \n",
       "3                             1  ...                        1   \n",
       "4                             0  ...                        1   \n",
       "...                         ...  ...                      ...   \n",
       "56195                    129277  ...                   151860   \n",
       "56196                        46  ...                       49   \n",
       "56197                    900959  ...                  1304160   \n",
       "56198                         1  ...                        3   \n",
       "56199                         3  ...                        6   \n",
       "\n",
       "       GTEX-ZYFC-0526-SM-5GIDF  GTEX-ZYFD-0326-SM-5NQ8I  \\\n",
       "0                            1                        0   \n",
       "1                           69                       32   \n",
       "2                            0                        0   \n",
       "3                            1                        0   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   204304                   108419   \n",
       "56196                       90                       35   \n",
       "56197                   814191                   902797   \n",
       "56198                      224                        7   \n",
       "56199                        2                       57   \n",
       "\n",
       "       GTEX-ZYFG-2426-SM-5GIE8  GTEX-ZYT6-1626-SM-5E45R  \\\n",
       "0                            0                        0   \n",
       "1                           47                       27   \n",
       "2                            0                        0   \n",
       "3                            0                        0   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   365195                   133850   \n",
       "56196                      189                       17   \n",
       "56197                  1181827                  1237537   \n",
       "56198                        7                        1   \n",
       "56199                      276                        1   \n",
       "\n",
       "       GTEX-ZYW4-0526-SM-5GZZ5  GTEX-ZYY3-0526-SM-5E45G  \\\n",
       "0                            0                        0   \n",
       "1                           44                       65   \n",
       "2                            0                        0   \n",
       "3                            0                        1   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   247638                   119170   \n",
       "56196                      102                       45   \n",
       "56197                   644574                  1027530   \n",
       "56198                        4                        7   \n",
       "56199                        4                        3   \n",
       "\n",
       "       GTEX-ZZ64-1526-SM-5E43K  GTEX-ZZPT-0626-SM-5GZXT  \\\n",
       "0                            0                        1   \n",
       "1                           74                       99   \n",
       "2                            0                        0   \n",
       "3                            0                        2   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   294986                    37886   \n",
       "56196                      151                        8   \n",
       "56197                  1084657                   680051   \n",
       "56198                        6                        1   \n",
       "56199                        4                        1   \n",
       "\n",
       "       GTEX-ZZPU-2626-SM-5E45Y  \n",
       "0                            1  \n",
       "1                           34  \n",
       "2                            0  \n",
       "3                            0  \n",
       "4                            0  \n",
       "...                        ...  \n",
       "56195                   303816  \n",
       "56196                      120  \n",
       "56197                  1231647  \n",
       "56198                       93  \n",
       "56199                        9  \n",
       "\n",
       "[56200 rows x 805 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GTEx_muscle = pd.read_table(\"GTEx data/gene_reads_muscle_skeletal.txt\")\n",
    "GTEx_muscle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "Muscle_sample_list = GTEx_muscle.columns[2:].tolist()\n",
    "Muscle_sample_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [],
   "source": [
    "SampleInfo = pd.DataFrame({'SampleID': Muscle_sample_list})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SampleID</th>\n",
       "      <th>SUBJID</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GTEX-1117F-0426-SM-5EGHI</td>\n",
       "      <td>GTEX-1117F</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GTEX-111CU-2026-SM-5GZZC</td>\n",
       "      <td>GTEX-111CU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GTEX-111FC-0326-SM-5GZZ1</td>\n",
       "      <td>GTEX-111FC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GTEX-111VG-2626-SM-5GZY2</td>\n",
       "      <td>GTEX-111VG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GTEX-111YS-2326-SM-5987L</td>\n",
       "      <td>GTEX-111YS</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>798</th>\n",
       "      <td>GTEX-ZYW4-0526-SM-5GZZ5</td>\n",
       "      <td>GTEX-ZYW4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>799</th>\n",
       "      <td>GTEX-ZYY3-0526-SM-5E45G</td>\n",
       "      <td>GTEX-ZYY3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>800</th>\n",
       "      <td>GTEX-ZZ64-1526-SM-5E43K</td>\n",
       "      <td>GTEX-ZZ64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>801</th>\n",
       "      <td>GTEX-ZZPT-0626-SM-5GZXT</td>\n",
       "      <td>GTEX-ZZPT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>802</th>\n",
       "      <td>GTEX-ZZPU-2626-SM-5E45Y</td>\n",
       "      <td>GTEX-ZZPU</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>803 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                     SampleID      SUBJID\n",
       "0    GTEX-1117F-0426-SM-5EGHI  GTEX-1117F\n",
       "1    GTEX-111CU-2026-SM-5GZZC  GTEX-111CU\n",
       "2    GTEX-111FC-0326-SM-5GZZ1  GTEX-111FC\n",
       "3    GTEX-111VG-2626-SM-5GZY2  GTEX-111VG\n",
       "4    GTEX-111YS-2326-SM-5987L  GTEX-111YS\n",
       "..                        ...         ...\n",
       "798   GTEX-ZYW4-0526-SM-5GZZ5   GTEX-ZYW4\n",
       "799   GTEX-ZYY3-0526-SM-5E45G   GTEX-ZYY3\n",
       "800   GTEX-ZZ64-1526-SM-5E43K   GTEX-ZZ64\n",
       "801   GTEX-ZZPT-0626-SM-5GZXT   GTEX-ZZPT\n",
       "802   GTEX-ZZPU-2626-SM-5E45Y   GTEX-ZZPU\n",
       "\n",
       "[803 rows x 2 columns]"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "SampleInfo['SUBJID']=SampleInfo['SampleID'].str.extract(r'(GTEX-.+(?=-\\d\\d\\d\\d-))')\n",
    "SampleInfo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SUBJID</th>\n",
       "      <th>SEX</th>\n",
       "      <th>AGE</th>\n",
       "      <th>DTHHRDY</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GTEX-1117F</td>\n",
       "      <td>2</td>\n",
       "      <td>60-69</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GTEX-111CU</td>\n",
       "      <td>1</td>\n",
       "      <td>50-59</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GTEX-111FC</td>\n",
       "      <td>1</td>\n",
       "      <td>60-69</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GTEX-111VG</td>\n",
       "      <td>1</td>\n",
       "      <td>60-69</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GTEX-111YS</td>\n",
       "      <td>1</td>\n",
       "      <td>60-69</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>975</th>\n",
       "      <td>GTEX-ZYY3</td>\n",
       "      <td>2</td>\n",
       "      <td>60-69</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>976</th>\n",
       "      <td>GTEX-ZZ64</td>\n",
       "      <td>1</td>\n",
       "      <td>20-29</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>977</th>\n",
       "      <td>GTEX-ZZPT</td>\n",
       "      <td>1</td>\n",
       "      <td>50-59</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>978</th>\n",
       "      <td>GTEX-ZZPU</td>\n",
       "      <td>2</td>\n",
       "      <td>50-59</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>979</th>\n",
       "      <td>K-562</td>\n",
       "      <td>2</td>\n",
       "      <td>50-59</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>980 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         SUBJID  SEX    AGE  DTHHRDY\n",
       "0    GTEX-1117F    2  60-69      4.0\n",
       "1    GTEX-111CU    1  50-59      0.0\n",
       "2    GTEX-111FC    1  60-69      1.0\n",
       "3    GTEX-111VG    1  60-69      3.0\n",
       "4    GTEX-111YS    1  60-69      0.0\n",
       "..          ...  ...    ...      ...\n",
       "975   GTEX-ZYY3    2  60-69      4.0\n",
       "976   GTEX-ZZ64    1  20-29      0.0\n",
       "977   GTEX-ZZPT    1  50-59      4.0\n",
       "978   GTEX-ZZPU    2  50-59      0.0\n",
       "979       K-562    2  50-59      NaN\n",
       "\n",
       "[980 rows x 4 columns]"
      ]
     },
     "execution_count": 77,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GTEx_anno = pd.read_table(\"GTEx data/GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt\")\n",
    "GTEx_anno['SEX'] = GTEx_anno['SEX'].map({1: 'M', 2: 'F'})\n",
    "GTEx_anno"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.merge(SampleInfo, GTEx_anno, how='left', on='SUBJID').to_csv('GTEx_name_list.csv', encoding='utf_8_sig', index=False)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Combine all GEO"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE115650 DUX4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>01-0021</th>\n",
       "      <th>01-0022-1</th>\n",
       "      <th>01-0023</th>\n",
       "      <th>01-0024</th>\n",
       "      <th>01-0025</th>\n",
       "      <th>01-0026</th>\n",
       "      <th>01-0027</th>\n",
       "      <th>01-0029</th>\n",
       "      <th>01-0030</th>\n",
       "      <th>...</th>\n",
       "      <th>32-0010</th>\n",
       "      <th>32-0011</th>\n",
       "      <th>32-0012</th>\n",
       "      <th>32-0013</th>\n",
       "      <th>32-0014</th>\n",
       "      <th>32-0015</th>\n",
       "      <th>32-0016</th>\n",
       "      <th>32-0017</th>\n",
       "      <th>32-0018</th>\n",
       "      <th>32-0019</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000000003</td>\n",
       "      <td>125</td>\n",
       "      <td>401</td>\n",
       "      <td>282</td>\n",
       "      <td>379</td>\n",
       "      <td>608</td>\n",
       "      <td>362</td>\n",
       "      <td>543</td>\n",
       "      <td>447</td>\n",
       "      <td>494</td>\n",
       "      <td>...</td>\n",
       "      <td>342</td>\n",
       "      <td>251</td>\n",
       "      <td>312</td>\n",
       "      <td>349</td>\n",
       "      <td>206</td>\n",
       "      <td>90</td>\n",
       "      <td>562</td>\n",
       "      <td>178</td>\n",
       "      <td>111</td>\n",
       "      <td>68</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000000005</td>\n",
       "      <td>37</td>\n",
       "      <td>564</td>\n",
       "      <td>57</td>\n",
       "      <td>2</td>\n",
       "      <td>953</td>\n",
       "      <td>99</td>\n",
       "      <td>398</td>\n",
       "      <td>594</td>\n",
       "      <td>2047</td>\n",
       "      <td>...</td>\n",
       "      <td>16</td>\n",
       "      <td>20</td>\n",
       "      <td>332</td>\n",
       "      <td>538</td>\n",
       "      <td>51</td>\n",
       "      <td>1</td>\n",
       "      <td>1077</td>\n",
       "      <td>139</td>\n",
       "      <td>7</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000000419</td>\n",
       "      <td>570</td>\n",
       "      <td>744</td>\n",
       "      <td>1968</td>\n",
       "      <td>1630</td>\n",
       "      <td>1503</td>\n",
       "      <td>1763</td>\n",
       "      <td>1226</td>\n",
       "      <td>1215</td>\n",
       "      <td>1569</td>\n",
       "      <td>...</td>\n",
       "      <td>1464</td>\n",
       "      <td>1432</td>\n",
       "      <td>1594</td>\n",
       "      <td>1648</td>\n",
       "      <td>1910</td>\n",
       "      <td>457</td>\n",
       "      <td>353</td>\n",
       "      <td>519</td>\n",
       "      <td>478</td>\n",
       "      <td>483</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000000457</td>\n",
       "      <td>173</td>\n",
       "      <td>323</td>\n",
       "      <td>360</td>\n",
       "      <td>266</td>\n",
       "      <td>578</td>\n",
       "      <td>426</td>\n",
       "      <td>423</td>\n",
       "      <td>320</td>\n",
       "      <td>476</td>\n",
       "      <td>...</td>\n",
       "      <td>458</td>\n",
       "      <td>352</td>\n",
       "      <td>470</td>\n",
       "      <td>384</td>\n",
       "      <td>315</td>\n",
       "      <td>157</td>\n",
       "      <td>221</td>\n",
       "      <td>173</td>\n",
       "      <td>196</td>\n",
       "      <td>157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000000460</td>\n",
       "      <td>22</td>\n",
       "      <td>46</td>\n",
       "      <td>36</td>\n",
       "      <td>17</td>\n",
       "      <td>136</td>\n",
       "      <td>61</td>\n",
       "      <td>103</td>\n",
       "      <td>54</td>\n",
       "      <td>97</td>\n",
       "      <td>...</td>\n",
       "      <td>43</td>\n",
       "      <td>53</td>\n",
       "      <td>70</td>\n",
       "      <td>53</td>\n",
       "      <td>20</td>\n",
       "      <td>11</td>\n",
       "      <td>83</td>\n",
       "      <td>43</td>\n",
       "      <td>17</td>\n",
       "      <td>30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27501</th>\n",
       "      <td>ENSG00000283075</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27502</th>\n",
       "      <td>ENSG00000283078</td>\n",
       "      <td>13</td>\n",
       "      <td>51</td>\n",
       "      <td>24</td>\n",
       "      <td>46</td>\n",
       "      <td>37</td>\n",
       "      <td>52</td>\n",
       "      <td>82</td>\n",
       "      <td>90</td>\n",
       "      <td>25</td>\n",
       "      <td>...</td>\n",
       "      <td>22</td>\n",
       "      <td>27</td>\n",
       "      <td>69</td>\n",
       "      <td>60</td>\n",
       "      <td>25</td>\n",
       "      <td>11</td>\n",
       "      <td>3</td>\n",
       "      <td>22</td>\n",
       "      <td>15</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27503</th>\n",
       "      <td>ENSG00000283103</td>\n",
       "      <td>28</td>\n",
       "      <td>48</td>\n",
       "      <td>83</td>\n",
       "      <td>72</td>\n",
       "      <td>72</td>\n",
       "      <td>69</td>\n",
       "      <td>95</td>\n",
       "      <td>79</td>\n",
       "      <td>100</td>\n",
       "      <td>...</td>\n",
       "      <td>74</td>\n",
       "      <td>58</td>\n",
       "      <td>95</td>\n",
       "      <td>92</td>\n",
       "      <td>145</td>\n",
       "      <td>41</td>\n",
       "      <td>33</td>\n",
       "      <td>42</td>\n",
       "      <td>34</td>\n",
       "      <td>35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27504</th>\n",
       "      <td>ENSG00000283108</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>14</td>\n",
       "      <td>4</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27505</th>\n",
       "      <td>ENSG00000283122</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27506 rows × 44 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  01-0021  01-0022-1  01-0023  01-0024  01-0025  \\\n",
       "0      ENSG00000000003      125        401      282      379      608   \n",
       "1      ENSG00000000005       37        564       57        2      953   \n",
       "2      ENSG00000000419      570        744     1968     1630     1503   \n",
       "3      ENSG00000000457      173        323      360      266      578   \n",
       "4      ENSG00000000460       22         46       36       17      136   \n",
       "...                ...      ...        ...      ...      ...      ...   \n",
       "27501  ENSG00000283075        1          5        0        0        2   \n",
       "27502  ENSG00000283078       13         51       24       46       37   \n",
       "27503  ENSG00000283103       28         48       83       72       72   \n",
       "27504  ENSG00000283108        3          2        5        3        2   \n",
       "27505  ENSG00000283122        3          0        4        0        3   \n",
       "\n",
       "       01-0026  01-0027  01-0029  01-0030  ...  32-0010  32-0011  32-0012  \\\n",
       "0          362      543      447      494  ...      342      251      312   \n",
       "1           99      398      594     2047  ...       16       20      332   \n",
       "2         1763     1226     1215     1569  ...     1464     1432     1594   \n",
       "3          426      423      320      476  ...      458      352      470   \n",
       "4           61      103       54       97  ...       43       53       70   \n",
       "...        ...      ...      ...      ...  ...      ...      ...      ...   \n",
       "27501        8        0        9        2  ...        3        4        0   \n",
       "27502       52       82       90       25  ...       22       27       69   \n",
       "27503       69       95       79      100  ...       74       58       95   \n",
       "27504        1        0       14        4  ...        2        0        5   \n",
       "27505        1        2        7        1  ...        4        0        0   \n",
       "\n",
       "       32-0013  32-0014  32-0015  32-0016  32-0017  32-0018  32-0019  \n",
       "0          349      206       90      562      178      111       68  \n",
       "1          538       51        1     1077      139        7        3  \n",
       "2         1648     1910      457      353      519      478      483  \n",
       "3          384      315      157      221      173      196      157  \n",
       "4           53       20       11       83       43       17       30  \n",
       "...        ...      ...      ...      ...      ...      ...      ...  \n",
       "27501        1        0        0        4        0        0        0  \n",
       "27502       60       25       11        3       22       15       11  \n",
       "27503       92      145       41       33       42       34       35  \n",
       "27504        0        2        1        2        1        1        0  \n",
       "27505        6        2        0        4        2        2        0  \n",
       "\n",
       "[27506 rows x 44 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE115650 = pd.read_csv(\"GEO data/GSE115650_biopsy_genecounts.csv\")\n",
    "GSE115650.GeneID = GSE115650.GeneID.str.extract(r'(ENSG.+(?=\\.))')\n",
    "GSE115650"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>01-0021</th>\n",
       "      <th>01-0022-1</th>\n",
       "      <th>01-0023</th>\n",
       "      <th>01-0024</th>\n",
       "      <th>01-0025</th>\n",
       "      <th>01-0026</th>\n",
       "      <th>01-0027</th>\n",
       "      <th>01-0029</th>\n",
       "      <th>01-0030</th>\n",
       "      <th>01-0032</th>\n",
       "      <th>...</th>\n",
       "      <th>32-0010</th>\n",
       "      <th>32-0011</th>\n",
       "      <th>32-0012</th>\n",
       "      <th>32-0013</th>\n",
       "      <th>32-0014</th>\n",
       "      <th>32-0015</th>\n",
       "      <th>32-0016</th>\n",
       "      <th>32-0017</th>\n",
       "      <th>32-0018</th>\n",
       "      <th>32-0019</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>count</th>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>27506.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>27506.000000</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "      <td>2.750600e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>mean</th>\n",
       "      <td>1.091320e+03</td>\n",
       "      <td>2.598315e+03</td>\n",
       "      <td>2.607463e+03</td>\n",
       "      <td>2.174435e+03</td>\n",
       "      <td>2.454144e+03</td>\n",
       "      <td>2.329753e+03</td>\n",
       "      <td>2.614001e+03</td>\n",
       "      <td>2.351584e+03</td>\n",
       "      <td>2.735142e+03</td>\n",
       "      <td>987.127427</td>\n",
       "      <td>...</td>\n",
       "      <td>2.734799e+03</td>\n",
       "      <td>2.470356e+03</td>\n",
       "      <td>2.674439e+03</td>\n",
       "      <td>2.711068e+03</td>\n",
       "      <td>2.506968e+03</td>\n",
       "      <td>1.097809e+03</td>\n",
       "      <td>726.399985</td>\n",
       "      <td>8.798460e+02</td>\n",
       "      <td>1.079375e+03</td>\n",
       "      <td>1.028396e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>std</th>\n",
       "      <td>1.784376e+04</td>\n",
       "      <td>3.847621e+04</td>\n",
       "      <td>5.252508e+04</td>\n",
       "      <td>4.147841e+04</td>\n",
       "      <td>2.984594e+04</td>\n",
       "      <td>3.476004e+04</td>\n",
       "      <td>3.864519e+04</td>\n",
       "      <td>3.485055e+04</td>\n",
       "      <td>3.952600e+04</td>\n",
       "      <td>14217.254243</td>\n",
       "      <td>...</td>\n",
       "      <td>4.674930e+04</td>\n",
       "      <td>4.076783e+04</td>\n",
       "      <td>4.360615e+04</td>\n",
       "      <td>4.891707e+04</td>\n",
       "      <td>4.582240e+04</td>\n",
       "      <td>1.838759e+04</td>\n",
       "      <td>5829.867576</td>\n",
       "      <td>1.170803e+04</td>\n",
       "      <td>1.827879e+04</td>\n",
       "      <td>1.570511e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>min</th>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25%</th>\n",
       "      <td>2.000000e+00</td>\n",
       "      <td>4.000000e+00</td>\n",
       "      <td>2.000000e+00</td>\n",
       "      <td>2.000000e+00</td>\n",
       "      <td>8.000000e+00</td>\n",
       "      <td>4.000000e+00</td>\n",
       "      <td>7.000000e+00</td>\n",
       "      <td>5.000000e+00</td>\n",
       "      <td>5.000000e+00</td>\n",
       "      <td>2.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>4.000000e+00</td>\n",
       "      <td>3.000000e+00</td>\n",
       "      <td>3.000000e+00</td>\n",
       "      <td>3.000000e+00</td>\n",
       "      <td>2.000000e+00</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>3.000000</td>\n",
       "      <td>2.000000e+00</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>1.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50%</th>\n",
       "      <td>2.600000e+01</td>\n",
       "      <td>6.600000e+01</td>\n",
       "      <td>4.100000e+01</td>\n",
       "      <td>4.000000e+01</td>\n",
       "      <td>1.190000e+02</td>\n",
       "      <td>6.800000e+01</td>\n",
       "      <td>1.060000e+02</td>\n",
       "      <td>8.900000e+01</td>\n",
       "      <td>8.600000e+01</td>\n",
       "      <td>25.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>5.900000e+01</td>\n",
       "      <td>5.400000e+01</td>\n",
       "      <td>5.800000e+01</td>\n",
       "      <td>5.500000e+01</td>\n",
       "      <td>5.200000e+01</td>\n",
       "      <td>2.000000e+01</td>\n",
       "      <td>54.000000</td>\n",
       "      <td>3.800000e+01</td>\n",
       "      <td>2.100000e+01</td>\n",
       "      <td>2.000000e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75%</th>\n",
       "      <td>3.280000e+02</td>\n",
       "      <td>8.537500e+02</td>\n",
       "      <td>6.360000e+02</td>\n",
       "      <td>5.580000e+02</td>\n",
       "      <td>1.198000e+03</td>\n",
       "      <td>8.680000e+02</td>\n",
       "      <td>1.015750e+03</td>\n",
       "      <td>8.597500e+02</td>\n",
       "      <td>1.019000e+03</td>\n",
       "      <td>312.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>7.500000e+02</td>\n",
       "      <td>7.230000e+02</td>\n",
       "      <td>8.200000e+02</td>\n",
       "      <td>7.260000e+02</td>\n",
       "      <td>6.230000e+02</td>\n",
       "      <td>2.920000e+02</td>\n",
       "      <td>492.000000</td>\n",
       "      <td>3.940000e+02</td>\n",
       "      <td>2.867500e+02</td>\n",
       "      <td>2.940000e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>max</th>\n",
       "      <td>1.526720e+06</td>\n",
       "      <td>3.246000e+06</td>\n",
       "      <td>5.768586e+06</td>\n",
       "      <td>4.312622e+06</td>\n",
       "      <td>2.505432e+06</td>\n",
       "      <td>3.422660e+06</td>\n",
       "      <td>3.499413e+06</td>\n",
       "      <td>2.579228e+06</td>\n",
       "      <td>3.697385e+06</td>\n",
       "      <td>950260.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>3.849836e+06</td>\n",
       "      <td>3.565972e+06</td>\n",
       "      <td>3.978545e+06</td>\n",
       "      <td>5.228409e+06</td>\n",
       "      <td>4.151291e+06</td>\n",
       "      <td>1.523883e+06</td>\n",
       "      <td>433706.000000</td>\n",
       "      <td>1.083653e+06</td>\n",
       "      <td>1.627194e+06</td>\n",
       "      <td>1.236857e+06</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8 rows × 43 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            01-0021     01-0022-1       01-0023       01-0024       01-0025  \\\n",
       "count  2.750600e+04  2.750600e+04  2.750600e+04  2.750600e+04  2.750600e+04   \n",
       "mean   1.091320e+03  2.598315e+03  2.607463e+03  2.174435e+03  2.454144e+03   \n",
       "std    1.784376e+04  3.847621e+04  5.252508e+04  4.147841e+04  2.984594e+04   \n",
       "min    0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "25%    2.000000e+00  4.000000e+00  2.000000e+00  2.000000e+00  8.000000e+00   \n",
       "50%    2.600000e+01  6.600000e+01  4.100000e+01  4.000000e+01  1.190000e+02   \n",
       "75%    3.280000e+02  8.537500e+02  6.360000e+02  5.580000e+02  1.198000e+03   \n",
       "max    1.526720e+06  3.246000e+06  5.768586e+06  4.312622e+06  2.505432e+06   \n",
       "\n",
       "            01-0026       01-0027       01-0029       01-0030        01-0032  \\\n",
       "count  2.750600e+04  2.750600e+04  2.750600e+04  2.750600e+04   27506.000000   \n",
       "mean   2.329753e+03  2.614001e+03  2.351584e+03  2.735142e+03     987.127427   \n",
       "std    3.476004e+04  3.864519e+04  3.485055e+04  3.952600e+04   14217.254243   \n",
       "min    0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00       0.000000   \n",
       "25%    4.000000e+00  7.000000e+00  5.000000e+00  5.000000e+00       2.000000   \n",
       "50%    6.800000e+01  1.060000e+02  8.900000e+01  8.600000e+01      25.000000   \n",
       "75%    8.680000e+02  1.015750e+03  8.597500e+02  1.019000e+03     312.000000   \n",
       "max    3.422660e+06  3.499413e+06  2.579228e+06  3.697385e+06  950260.000000   \n",
       "\n",
       "       ...       32-0010       32-0011       32-0012       32-0013  \\\n",
       "count  ...  2.750600e+04  2.750600e+04  2.750600e+04  2.750600e+04   \n",
       "mean   ...  2.734799e+03  2.470356e+03  2.674439e+03  2.711068e+03   \n",
       "std    ...  4.674930e+04  4.076783e+04  4.360615e+04  4.891707e+04   \n",
       "min    ...  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "25%    ...  4.000000e+00  3.000000e+00  3.000000e+00  3.000000e+00   \n",
       "50%    ...  5.900000e+01  5.400000e+01  5.800000e+01  5.500000e+01   \n",
       "75%    ...  7.500000e+02  7.230000e+02  8.200000e+02  7.260000e+02   \n",
       "max    ...  3.849836e+06  3.565972e+06  3.978545e+06  5.228409e+06   \n",
       "\n",
       "            32-0014       32-0015        32-0016       32-0017       32-0018  \\\n",
       "count  2.750600e+04  2.750600e+04   27506.000000  2.750600e+04  2.750600e+04   \n",
       "mean   2.506968e+03  1.097809e+03     726.399985  8.798460e+02  1.079375e+03   \n",
       "std    4.582240e+04  1.838759e+04    5829.867576  1.170803e+04  1.827879e+04   \n",
       "min    0.000000e+00  0.000000e+00       0.000000  0.000000e+00  0.000000e+00   \n",
       "25%    2.000000e+00  1.000000e+00       3.000000  2.000000e+00  1.000000e+00   \n",
       "50%    5.200000e+01  2.000000e+01      54.000000  3.800000e+01  2.100000e+01   \n",
       "75%    6.230000e+02  2.920000e+02     492.000000  3.940000e+02  2.867500e+02   \n",
       "max    4.151291e+06  1.523883e+06  433706.000000  1.083653e+06  1.627194e+06   \n",
       "\n",
       "            32-0019  \n",
       "count  2.750600e+04  \n",
       "mean   1.028396e+03  \n",
       "std    1.570511e+04  \n",
       "min    0.000000e+00  \n",
       "25%    1.000000e+00  \n",
       "50%    2.000000e+01  \n",
       "75%    2.940000e+02  \n",
       "max    1.236857e+06  \n",
       "\n",
       "[8 rows x 43 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE115650.describe()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE140261 DUX4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>01-0041_II</th>\n",
       "      <th>01-0042_II</th>\n",
       "      <th>01-0043_II</th>\n",
       "      <th>01-0044_II</th>\n",
       "      <th>01-0045_II</th>\n",
       "      <th>01-0046_II</th>\n",
       "      <th>01-0048_II</th>\n",
       "      <th>01-0049_II</th>\n",
       "      <th>01-0022b_II</th>\n",
       "      <th>...</th>\n",
       "      <th>32-0007b_II</th>\n",
       "      <th>32-0009b_II</th>\n",
       "      <th>32-0010b_II</th>\n",
       "      <th>32-0012b_II</th>\n",
       "      <th>32-0013b_II</th>\n",
       "      <th>32-0014b_II</th>\n",
       "      <th>32-0015b_II</th>\n",
       "      <th>32-0016b_II</th>\n",
       "      <th>32-0017b_II</th>\n",
       "      <th>32-0018b_II</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000000003</td>\n",
       "      <td>375</td>\n",
       "      <td>253</td>\n",
       "      <td>330</td>\n",
       "      <td>321</td>\n",
       "      <td>366</td>\n",
       "      <td>113</td>\n",
       "      <td>335</td>\n",
       "      <td>98</td>\n",
       "      <td>388</td>\n",
       "      <td>...</td>\n",
       "      <td>463</td>\n",
       "      <td>235</td>\n",
       "      <td>1630</td>\n",
       "      <td>1598</td>\n",
       "      <td>284</td>\n",
       "      <td>325</td>\n",
       "      <td>315</td>\n",
       "      <td>792</td>\n",
       "      <td>230</td>\n",
       "      <td>549</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000000005</td>\n",
       "      <td>4</td>\n",
       "      <td>6</td>\n",
       "      <td>9</td>\n",
       "      <td>4</td>\n",
       "      <td>27</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>640</td>\n",
       "      <td>...</td>\n",
       "      <td>209</td>\n",
       "      <td>34</td>\n",
       "      <td>5843</td>\n",
       "      <td>414</td>\n",
       "      <td>74</td>\n",
       "      <td>208</td>\n",
       "      <td>16</td>\n",
       "      <td>102</td>\n",
       "      <td>35</td>\n",
       "      <td>457</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000000419</td>\n",
       "      <td>1779</td>\n",
       "      <td>1178</td>\n",
       "      <td>1457</td>\n",
       "      <td>1934</td>\n",
       "      <td>1511</td>\n",
       "      <td>550</td>\n",
       "      <td>1976</td>\n",
       "      <td>577</td>\n",
       "      <td>721</td>\n",
       "      <td>...</td>\n",
       "      <td>1428</td>\n",
       "      <td>1038</td>\n",
       "      <td>1221</td>\n",
       "      <td>1431</td>\n",
       "      <td>1302</td>\n",
       "      <td>1721</td>\n",
       "      <td>1480</td>\n",
       "      <td>1111</td>\n",
       "      <td>1251</td>\n",
       "      <td>1414</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000000457</td>\n",
       "      <td>373</td>\n",
       "      <td>629</td>\n",
       "      <td>493</td>\n",
       "      <td>598</td>\n",
       "      <td>482</td>\n",
       "      <td>154</td>\n",
       "      <td>464</td>\n",
       "      <td>137</td>\n",
       "      <td>187</td>\n",
       "      <td>...</td>\n",
       "      <td>402</td>\n",
       "      <td>424</td>\n",
       "      <td>560</td>\n",
       "      <td>597</td>\n",
       "      <td>342</td>\n",
       "      <td>435</td>\n",
       "      <td>356</td>\n",
       "      <td>689</td>\n",
       "      <td>311</td>\n",
       "      <td>560</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000000460</td>\n",
       "      <td>56</td>\n",
       "      <td>55</td>\n",
       "      <td>40</td>\n",
       "      <td>48</td>\n",
       "      <td>27</td>\n",
       "      <td>8</td>\n",
       "      <td>49</td>\n",
       "      <td>16</td>\n",
       "      <td>17</td>\n",
       "      <td>...</td>\n",
       "      <td>56</td>\n",
       "      <td>48</td>\n",
       "      <td>145</td>\n",
       "      <td>149</td>\n",
       "      <td>37</td>\n",
       "      <td>85</td>\n",
       "      <td>61</td>\n",
       "      <td>187</td>\n",
       "      <td>40</td>\n",
       "      <td>112</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30713</th>\n",
       "      <td>ENSG00000283078</td>\n",
       "      <td>22</td>\n",
       "      <td>32</td>\n",
       "      <td>31</td>\n",
       "      <td>47</td>\n",
       "      <td>24</td>\n",
       "      <td>21</td>\n",
       "      <td>26</td>\n",
       "      <td>21</td>\n",
       "      <td>31</td>\n",
       "      <td>...</td>\n",
       "      <td>46</td>\n",
       "      <td>42</td>\n",
       "      <td>29</td>\n",
       "      <td>34</td>\n",
       "      <td>38</td>\n",
       "      <td>62</td>\n",
       "      <td>42</td>\n",
       "      <td>42</td>\n",
       "      <td>25</td>\n",
       "      <td>54</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30714</th>\n",
       "      <td>ENSG00000283098</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30715</th>\n",
       "      <td>ENSG00000283103</td>\n",
       "      <td>78</td>\n",
       "      <td>64</td>\n",
       "      <td>63</td>\n",
       "      <td>58</td>\n",
       "      <td>70</td>\n",
       "      <td>17</td>\n",
       "      <td>62</td>\n",
       "      <td>43</td>\n",
       "      <td>105</td>\n",
       "      <td>...</td>\n",
       "      <td>74</td>\n",
       "      <td>60</td>\n",
       "      <td>182</td>\n",
       "      <td>101</td>\n",
       "      <td>76</td>\n",
       "      <td>86</td>\n",
       "      <td>63</td>\n",
       "      <td>73</td>\n",
       "      <td>73</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30716</th>\n",
       "      <td>ENSG00000283108</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>12</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30717</th>\n",
       "      <td>ENSG00000283122</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>30718 rows × 36 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  01-0041_II  01-0042_II  01-0043_II  01-0044_II  \\\n",
       "0      ENSG00000000003         375         253         330         321   \n",
       "1      ENSG00000000005           4           6           9           4   \n",
       "2      ENSG00000000419        1779        1178        1457        1934   \n",
       "3      ENSG00000000457         373         629         493         598   \n",
       "4      ENSG00000000460          56          55          40          48   \n",
       "...                ...         ...         ...         ...         ...   \n",
       "30713  ENSG00000283078          22          32          31          47   \n",
       "30714  ENSG00000283098           0           0           0           0   \n",
       "30715  ENSG00000283103          78          64          63          58   \n",
       "30716  ENSG00000283108           2           7           2           2   \n",
       "30717  ENSG00000283122           0           2           5           1   \n",
       "\n",
       "       01-0045_II  01-0046_II  01-0048_II  01-0049_II  01-0022b_II  ...  \\\n",
       "0             366         113         335          98          388  ...   \n",
       "1              27           2           0           0          640  ...   \n",
       "2            1511         550        1976         577          721  ...   \n",
       "3             482         154         464         137          187  ...   \n",
       "4              27           8          49          16           17  ...   \n",
       "...           ...         ...         ...         ...          ...  ...   \n",
       "30713          24          21          26          21           31  ...   \n",
       "30714           0           0           3           0            0  ...   \n",
       "30715          70          17          62          43          105  ...   \n",
       "30716           0           2           3           0            7  ...   \n",
       "30717           3           1           1           1            0  ...   \n",
       "\n",
       "       32-0007b_II  32-0009b_II  32-0010b_II  32-0012b_II  32-0013b_II  \\\n",
       "0              463          235         1630         1598          284   \n",
       "1              209           34         5843          414           74   \n",
       "2             1428         1038         1221         1431         1302   \n",
       "3              402          424          560          597          342   \n",
       "4               56           48          145          149           37   \n",
       "...            ...          ...          ...          ...          ...   \n",
       "30713           46           42           29           34           38   \n",
       "30714            0            0            7            4            0   \n",
       "30715           74           60          182          101           76   \n",
       "30716            3            2            5            4            1   \n",
       "30717            5            1            7            6            4   \n",
       "\n",
       "       32-0014b_II  32-0015b_II  32-0016b_II  32-0017b_II  32-0018b_II  \n",
       "0              325          315          792          230          549  \n",
       "1              208           16          102           35          457  \n",
       "2             1721         1480         1111         1251         1414  \n",
       "3              435          356          689          311          560  \n",
       "4               85           61          187           40          112  \n",
       "...            ...          ...          ...          ...          ...  \n",
       "30713           62           42           42           25           54  \n",
       "30714            2            0            0            0            0  \n",
       "30715           86           63           73           73           60  \n",
       "30716            1            1           12            2            4  \n",
       "30717            0            1            2            0            2  \n",
       "\n",
       "[30718 rows x 36 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE140261 = pd.read_csv(\"GEO data/GSE140261_year2_genecounts.csv\")\n",
    "GSE140261.GeneID = GSE140261.GeneID.str.extract(r'(ENSG.+(?=\\.))')\n",
    "GSE140261"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE175861 DMD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>10869X3</th>\n",
       "      <th>11015X12</th>\n",
       "      <th>11183X8</th>\n",
       "      <th>11689X20</th>\n",
       "      <th>11689X23</th>\n",
       "      <th>13707X5</th>\n",
       "      <th>14857X11</th>\n",
       "      <th>14857X12</th>\n",
       "      <th>15357X4</th>\n",
       "      <th>16244X3</th>\n",
       "      <th>11885X6</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000155657</td>\n",
       "      <td>1918201</td>\n",
       "      <td>4390843</td>\n",
       "      <td>2939062</td>\n",
       "      <td>3188342</td>\n",
       "      <td>3252145</td>\n",
       "      <td>7140320</td>\n",
       "      <td>1603461</td>\n",
       "      <td>2035456</td>\n",
       "      <td>5976164</td>\n",
       "      <td>1657942</td>\n",
       "      <td>4273302</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000183091</td>\n",
       "      <td>277284</td>\n",
       "      <td>416079</td>\n",
       "      <td>457378</td>\n",
       "      <td>363313</td>\n",
       "      <td>354826</td>\n",
       "      <td>890461</td>\n",
       "      <td>277007</td>\n",
       "      <td>294192</td>\n",
       "      <td>618856</td>\n",
       "      <td>252068</td>\n",
       "      <td>430757</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000143632</td>\n",
       "      <td>47598</td>\n",
       "      <td>109625</td>\n",
       "      <td>150435</td>\n",
       "      <td>140192</td>\n",
       "      <td>141274</td>\n",
       "      <td>367091</td>\n",
       "      <td>424906</td>\n",
       "      <td>261527</td>\n",
       "      <td>493619</td>\n",
       "      <td>80493</td>\n",
       "      <td>254195</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000125414</td>\n",
       "      <td>60985</td>\n",
       "      <td>139826</td>\n",
       "      <td>172479</td>\n",
       "      <td>118133</td>\n",
       "      <td>197226</td>\n",
       "      <td>409384</td>\n",
       "      <td>353869</td>\n",
       "      <td>74081</td>\n",
       "      <td>164818</td>\n",
       "      <td>89271</td>\n",
       "      <td>160796</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000092054</td>\n",
       "      <td>69885</td>\n",
       "      <td>105429</td>\n",
       "      <td>102954</td>\n",
       "      <td>140388</td>\n",
       "      <td>110424</td>\n",
       "      <td>283640</td>\n",
       "      <td>101402</td>\n",
       "      <td>213352</td>\n",
       "      <td>320443</td>\n",
       "      <td>47102</td>\n",
       "      <td>166245</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20082</th>\n",
       "      <td>ENSG00000205775</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20083</th>\n",
       "      <td>ENSG00000196611</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20084</th>\n",
       "      <td>ENSG00000277322</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20085</th>\n",
       "      <td>ENSG00000169789</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20086</th>\n",
       "      <td>ENSG00000181761</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20087 rows × 12 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  10869X3  11015X12  11183X8  11689X20  11689X23  \\\n",
       "0      ENSG00000155657  1918201   4390843  2939062   3188342   3252145   \n",
       "1      ENSG00000183091   277284    416079   457378    363313    354826   \n",
       "2      ENSG00000143632    47598    109625   150435    140192    141274   \n",
       "3      ENSG00000125414    60985    139826   172479    118133    197226   \n",
       "4      ENSG00000092054    69885    105429   102954    140388    110424   \n",
       "...                ...      ...       ...      ...       ...       ...   \n",
       "20082  ENSG00000205775        0         0        0         0         0   \n",
       "20083  ENSG00000196611        0         0        0         0         0   \n",
       "20084  ENSG00000277322        0         0        0         0         0   \n",
       "20085  ENSG00000169789        0         0        0         0         0   \n",
       "20086  ENSG00000181761        0         0        0         0         0   \n",
       "\n",
       "       13707X5  14857X11  14857X12  15357X4  16244X3  11885X6  \n",
       "0      7140320   1603461   2035456  5976164  1657942  4273302  \n",
       "1       890461    277007    294192   618856   252068   430757  \n",
       "2       367091    424906    261527   493619    80493   254195  \n",
       "3       409384    353869     74081   164818    89271   160796  \n",
       "4       283640    101402    213352   320443    47102   166245  \n",
       "...        ...       ...       ...      ...      ...      ...  \n",
       "20082        0         0         0        0        0        0  \n",
       "20083        0         0         0        0        0        0  \n",
       "20084        0         0         0        0        0        0  \n",
       "20085        0         0         0        0        0        0  \n",
       "20086        0         0         0        0        0        0  \n",
       "\n",
       "[20087 rows x 12 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE175861 = pd.read_table(\"GEO data/GSE175861_FEATURECOUNTS_gencodeV31_PCnoMT_modified.txt\")\n",
    "GSE175861.drop(['GeneSymbol'], axis=1, inplace=True)\n",
    "GSE175861"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE184951 DMPK"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>Control-1</th>\n",
       "      <th>Control-12</th>\n",
       "      <th>Control-13</th>\n",
       "      <th>Control-2</th>\n",
       "      <th>Control-3</th>\n",
       "      <th>Control-4</th>\n",
       "      <th>Control-6</th>\n",
       "      <th>Control-7</th>\n",
       "      <th>Control-8</th>\n",
       "      <th>...</th>\n",
       "      <th>Pre-S12</th>\n",
       "      <th>Pre-S13</th>\n",
       "      <th>Pre-S2</th>\n",
       "      <th>Pre-S3</th>\n",
       "      <th>Pre-S4</th>\n",
       "      <th>Pre-S5</th>\n",
       "      <th>Pre-S6</th>\n",
       "      <th>Pre-S7</th>\n",
       "      <th>Pre-S8</th>\n",
       "      <th>Pre-S9</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000000003</td>\n",
       "      <td>104</td>\n",
       "      <td>127</td>\n",
       "      <td>161</td>\n",
       "      <td>140</td>\n",
       "      <td>133</td>\n",
       "      <td>83</td>\n",
       "      <td>123</td>\n",
       "      <td>104</td>\n",
       "      <td>80</td>\n",
       "      <td>...</td>\n",
       "      <td>137</td>\n",
       "      <td>102</td>\n",
       "      <td>136</td>\n",
       "      <td>115</td>\n",
       "      <td>104</td>\n",
       "      <td>111</td>\n",
       "      <td>205</td>\n",
       "      <td>134</td>\n",
       "      <td>92</td>\n",
       "      <td>206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000000005</td>\n",
       "      <td>9</td>\n",
       "      <td>17</td>\n",
       "      <td>679</td>\n",
       "      <td>16</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>21</td>\n",
       "      <td>16</td>\n",
       "      <td>17</td>\n",
       "      <td>...</td>\n",
       "      <td>14</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "      <td>9</td>\n",
       "      <td>33</td>\n",
       "      <td>2</td>\n",
       "      <td>275</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>93</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000000419</td>\n",
       "      <td>1609</td>\n",
       "      <td>1785</td>\n",
       "      <td>1542</td>\n",
       "      <td>1876</td>\n",
       "      <td>1398</td>\n",
       "      <td>2057</td>\n",
       "      <td>2433</td>\n",
       "      <td>1642</td>\n",
       "      <td>1614</td>\n",
       "      <td>...</td>\n",
       "      <td>759</td>\n",
       "      <td>842</td>\n",
       "      <td>530</td>\n",
       "      <td>714</td>\n",
       "      <td>658</td>\n",
       "      <td>709</td>\n",
       "      <td>562</td>\n",
       "      <td>881</td>\n",
       "      <td>801</td>\n",
       "      <td>880</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000000457</td>\n",
       "      <td>453</td>\n",
       "      <td>507</td>\n",
       "      <td>467</td>\n",
       "      <td>440</td>\n",
       "      <td>545</td>\n",
       "      <td>396</td>\n",
       "      <td>438</td>\n",
       "      <td>475</td>\n",
       "      <td>304</td>\n",
       "      <td>...</td>\n",
       "      <td>361</td>\n",
       "      <td>303</td>\n",
       "      <td>247</td>\n",
       "      <td>280</td>\n",
       "      <td>260</td>\n",
       "      <td>296</td>\n",
       "      <td>282</td>\n",
       "      <td>323</td>\n",
       "      <td>274</td>\n",
       "      <td>249</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000000460</td>\n",
       "      <td>122</td>\n",
       "      <td>128</td>\n",
       "      <td>161</td>\n",
       "      <td>140</td>\n",
       "      <td>138</td>\n",
       "      <td>94</td>\n",
       "      <td>108</td>\n",
       "      <td>152</td>\n",
       "      <td>49</td>\n",
       "      <td>...</td>\n",
       "      <td>90</td>\n",
       "      <td>88</td>\n",
       "      <td>93</td>\n",
       "      <td>74</td>\n",
       "      <td>68</td>\n",
       "      <td>87</td>\n",
       "      <td>99</td>\n",
       "      <td>94</td>\n",
       "      <td>53</td>\n",
       "      <td>101</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63671</th>\n",
       "      <td>ENSG00000273488</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>20</td>\n",
       "      <td>9</td>\n",
       "      <td>6</td>\n",
       "      <td>9</td>\n",
       "      <td>22</td>\n",
       "      <td>25</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>14</td>\n",
       "      <td>11</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63672</th>\n",
       "      <td>ENSG00000273489</td>\n",
       "      <td>19</td>\n",
       "      <td>6</td>\n",
       "      <td>20</td>\n",
       "      <td>48</td>\n",
       "      <td>22</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>23</td>\n",
       "      <td>6</td>\n",
       "      <td>...</td>\n",
       "      <td>12</td>\n",
       "      <td>18</td>\n",
       "      <td>10</td>\n",
       "      <td>12</td>\n",
       "      <td>5</td>\n",
       "      <td>10</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63673</th>\n",
       "      <td>ENSG00000273490</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63674</th>\n",
       "      <td>ENSG00000273491</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63675</th>\n",
       "      <td>ENSG00000273492</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>63676 rows × 33 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  Control-1  Control-12  Control-13  Control-2  \\\n",
       "0      ENSG00000000003        104         127         161        140   \n",
       "1      ENSG00000000005          9          17         679         16   \n",
       "2      ENSG00000000419       1609        1785        1542       1876   \n",
       "3      ENSG00000000457        453         507         467        440   \n",
       "4      ENSG00000000460        122         128         161        140   \n",
       "...                ...        ...         ...         ...        ...   \n",
       "63671  ENSG00000273488         12          12          20          9   \n",
       "63672  ENSG00000273489         19           6          20         48   \n",
       "63673  ENSG00000273490          0           0           0          0   \n",
       "63674  ENSG00000273491          0           0           0          0   \n",
       "63675  ENSG00000273492          2           3           2          3   \n",
       "\n",
       "       Control-3  Control-4  Control-6  Control-7  Control-8  ...  Pre-S12  \\\n",
       "0            133         83        123        104         80  ...      137   \n",
       "1              6          3         21         16         17  ...       14   \n",
       "2           1398       2057       2433       1642       1614  ...      759   \n",
       "3            545        396        438        475        304  ...      361   \n",
       "4            138         94        108        152         49  ...       90   \n",
       "...          ...        ...        ...        ...        ...  ...      ...   \n",
       "63671          6          9         22         25         10  ...        9   \n",
       "63672         22          8          8         23          6  ...       12   \n",
       "63673          0          0          0          0          0  ...        0   \n",
       "63674          0          0          0          0          0  ...        0   \n",
       "63675          0          0          0          1          0  ...        0   \n",
       "\n",
       "       Pre-S13  Pre-S2  Pre-S3  Pre-S4  Pre-S5  Pre-S6  Pre-S7  Pre-S8  Pre-S9  \n",
       "0          102     136     115     104     111     205     134      92     206  \n",
       "1           23      22       9      33       2     275       4       5      93  \n",
       "2          842     530     714     658     709     562     881     801     880  \n",
       "3          303     247     280     260     296     282     323     274     249  \n",
       "4           88      93      74      68      87      99      94      53     101  \n",
       "...        ...     ...     ...     ...     ...     ...     ...     ...     ...  \n",
       "63671        8       7       6      14      11       4       4       5      10  \n",
       "63672       18      10      12       5      10       2       5       6       7  \n",
       "63673        0       0       0       0       0       0       0       0       0  \n",
       "63674        0       0       0       0       0       0       0       0       0  \n",
       "63675        0       1       4       0       1       0       0       1       0  \n",
       "\n",
       "[63676 rows x 33 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE184951 = pd.read_csv(\"GEO data/GSE184951_rawcount.csv\")\n",
    "GSE184951.drop(['GeneSymbol'], axis=1, inplace=True)\n",
    "GSE184951"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE201255 DMPK"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>PeCo-19</th>\n",
       "      <th>PeCo-20</th>\n",
       "      <th>PeCo-21</th>\n",
       "      <th>AdCo-01</th>\n",
       "      <th>AdCo-02</th>\n",
       "      <th>AdCo-03</th>\n",
       "      <th>AdCo-04</th>\n",
       "      <th>AdCo-05</th>\n",
       "      <th>AdCo-06</th>\n",
       "      <th>AdCo-07</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000223972</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000227232</td>\n",
       "      <td>77</td>\n",
       "      <td>76</td>\n",
       "      <td>50</td>\n",
       "      <td>41</td>\n",
       "      <td>32</td>\n",
       "      <td>76</td>\n",
       "      <td>35</td>\n",
       "      <td>32</td>\n",
       "      <td>22</td>\n",
       "      <td>...</td>\n",
       "      <td>27</td>\n",
       "      <td>42</td>\n",
       "      <td>90</td>\n",
       "      <td>28</td>\n",
       "      <td>48</td>\n",
       "      <td>28</td>\n",
       "      <td>50</td>\n",
       "      <td>49</td>\n",
       "      <td>22</td>\n",
       "      <td>48</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267</td>\n",
       "      <td>19</td>\n",
       "      <td>20</td>\n",
       "      <td>21</td>\n",
       "      <td>7</td>\n",
       "      <td>8</td>\n",
       "      <td>10</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>8</td>\n",
       "      <td>22</td>\n",
       "      <td>6</td>\n",
       "      <td>11</td>\n",
       "      <td>5</td>\n",
       "      <td>13</td>\n",
       "      <td>10</td>\n",
       "      <td>4</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000284332</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60618</th>\n",
       "      <td>ENSG00000271254</td>\n",
       "      <td>1242</td>\n",
       "      <td>791</td>\n",
       "      <td>711</td>\n",
       "      <td>686</td>\n",
       "      <td>307</td>\n",
       "      <td>513</td>\n",
       "      <td>182</td>\n",
       "      <td>200</td>\n",
       "      <td>230</td>\n",
       "      <td>...</td>\n",
       "      <td>131</td>\n",
       "      <td>249</td>\n",
       "      <td>129</td>\n",
       "      <td>143</td>\n",
       "      <td>202</td>\n",
       "      <td>340</td>\n",
       "      <td>352</td>\n",
       "      <td>190</td>\n",
       "      <td>79</td>\n",
       "      <td>236</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60619</th>\n",
       "      <td>ENSG00000275405</td>\n",
       "      <td>12</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>6</td>\n",
       "      <td>5</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>7</td>\n",
       "      <td>...</td>\n",
       "      <td>5</td>\n",
       "      <td>2</td>\n",
       "      <td>22</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60620</th>\n",
       "      <td>ENSG00000275987</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>15</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60621</th>\n",
       "      <td>ENSG00000277475</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>10</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60622</th>\n",
       "      <td>ENSG00000268674</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>60623 rows × 87 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  \\\n",
       "0      ENSG00000223972       0       0       0       0       0       0   \n",
       "1      ENSG00000227232      77      76      50      41      32      76   \n",
       "2      ENSG00000278267      19      20      21       7       8      10   \n",
       "3      ENSG00000243485       0       0       0       0       0       0   \n",
       "4      ENSG00000284332       0       0       0       0       0       0   \n",
       "...                ...     ...     ...     ...     ...     ...     ...   \n",
       "60618  ENSG00000271254    1242     791     711     686     307     513   \n",
       "60619  ENSG00000275405      12       6       3       3       6       5   \n",
       "60620  ENSG00000275987       0       0       0       0       0       2   \n",
       "60621  ENSG00000277475       0       0       0       0       0       0   \n",
       "60622  ENSG00000268674       0       0       0       0       0       0   \n",
       "\n",
       "       CDM-07  CDM-08  CDM-09  ...  PeCo-19  PeCo-20  PeCo-21  AdCo-01  \\\n",
       "0           0       0       0  ...        0        0        0        0   \n",
       "1          35      32      22  ...       27       42       90       28   \n",
       "2           6       6       6  ...        1        8       22        6   \n",
       "3           0       0       0  ...        0        0        0        0   \n",
       "4           0       0       0  ...        0        0        0        0   \n",
       "...       ...     ...     ...  ...      ...      ...      ...      ...   \n",
       "60618     182     200     230  ...      131      249      129      143   \n",
       "60619       3       3       7  ...        5        2       22        4   \n",
       "60620       0       1       1  ...       15        1        0        0   \n",
       "60621       0       0       1  ...       10        0        0        0   \n",
       "60622       0       0       0  ...        0        0        0        0   \n",
       "\n",
       "       AdCo-02  AdCo-03  AdCo-04  AdCo-05  AdCo-06  AdCo-07  \n",
       "0            0        0        0        0        0        0  \n",
       "1           48       28       50       49       22       48  \n",
       "2           11        5       13       10        4        7  \n",
       "3            0        0        0        0        0        0  \n",
       "4            0        0        0        0        0        0  \n",
       "...        ...      ...      ...      ...      ...      ...  \n",
       "60618      202      340      352      190       79      236  \n",
       "60619        4        6        6        3        1        7  \n",
       "60620        0        0        0        0        0        1  \n",
       "60621        0        0        1        0        0        0  \n",
       "60622        0        0        0        0        0        0  \n",
       "\n",
       "[60623 rows x 87 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE201255 = pd.read_table(\"GEO data/GSE201255_raw_counts.txt\")\n",
    "GSE201255"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GSE202745 ANO5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>6@T</th>\n",
       "      <th>C01@T</th>\n",
       "      <th>C02@T</th>\n",
       "      <th>C03@T</th>\n",
       "      <th>C04@T</th>\n",
       "      <th>C05@T</th>\n",
       "      <th>C06@T</th>\n",
       "      <th>C07@T</th>\n",
       "      <th>C08@T</th>\n",
       "      <th>...</th>\n",
       "      <th>P38@T</th>\n",
       "      <th>P40@T</th>\n",
       "      <th>P41@T</th>\n",
       "      <th>P42@T</th>\n",
       "      <th>P43@T</th>\n",
       "      <th>P44@T</th>\n",
       "      <th>P45@T</th>\n",
       "      <th>P46@T</th>\n",
       "      <th>P47@T</th>\n",
       "      <th>P48@T</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000000003</td>\n",
       "      <td>518</td>\n",
       "      <td>45</td>\n",
       "      <td>32</td>\n",
       "      <td>51</td>\n",
       "      <td>46</td>\n",
       "      <td>36</td>\n",
       "      <td>31</td>\n",
       "      <td>43</td>\n",
       "      <td>34</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>147</td>\n",
       "      <td>72</td>\n",
       "      <td>67</td>\n",
       "      <td>70</td>\n",
       "      <td>37</td>\n",
       "      <td>106</td>\n",
       "      <td>17</td>\n",
       "      <td>51</td>\n",
       "      <td>66</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000000005</td>\n",
       "      <td>2479</td>\n",
       "      <td>22</td>\n",
       "      <td>3</td>\n",
       "      <td>11</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>9</td>\n",
       "      <td>3</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>29</td>\n",
       "      <td>28</td>\n",
       "      <td>6</td>\n",
       "      <td>37</td>\n",
       "      <td>2</td>\n",
       "      <td>27</td>\n",
       "      <td>21</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000000419</td>\n",
       "      <td>321</td>\n",
       "      <td>193</td>\n",
       "      <td>214</td>\n",
       "      <td>241</td>\n",
       "      <td>158</td>\n",
       "      <td>159</td>\n",
       "      <td>206</td>\n",
       "      <td>198</td>\n",
       "      <td>134</td>\n",
       "      <td>...</td>\n",
       "      <td>4</td>\n",
       "      <td>435</td>\n",
       "      <td>287</td>\n",
       "      <td>316</td>\n",
       "      <td>186</td>\n",
       "      <td>230</td>\n",
       "      <td>261</td>\n",
       "      <td>13</td>\n",
       "      <td>203</td>\n",
       "      <td>253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000000457</td>\n",
       "      <td>549</td>\n",
       "      <td>144</td>\n",
       "      <td>144</td>\n",
       "      <td>179</td>\n",
       "      <td>125</td>\n",
       "      <td>91</td>\n",
       "      <td>138</td>\n",
       "      <td>125</td>\n",
       "      <td>109</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>250</td>\n",
       "      <td>197</td>\n",
       "      <td>253</td>\n",
       "      <td>159</td>\n",
       "      <td>204</td>\n",
       "      <td>240</td>\n",
       "      <td>97</td>\n",
       "      <td>94</td>\n",
       "      <td>173</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000000460</td>\n",
       "      <td>150</td>\n",
       "      <td>25</td>\n",
       "      <td>32</td>\n",
       "      <td>49</td>\n",
       "      <td>13</td>\n",
       "      <td>9</td>\n",
       "      <td>22</td>\n",
       "      <td>21</td>\n",
       "      <td>32</td>\n",
       "      <td>...</td>\n",
       "      <td>4</td>\n",
       "      <td>72</td>\n",
       "      <td>31</td>\n",
       "      <td>47</td>\n",
       "      <td>48</td>\n",
       "      <td>35</td>\n",
       "      <td>55</td>\n",
       "      <td>19</td>\n",
       "      <td>29</td>\n",
       "      <td>43</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58228</th>\n",
       "      <td>ENSG00000284592</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58229</th>\n",
       "      <td>ENSG00000284594</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58230</th>\n",
       "      <td>ENSG00000284595</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58231</th>\n",
       "      <td>ENSG00000284596</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58232</th>\n",
       "      <td>ENSG00000284600</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>58233 rows × 85 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID   6@T  C01@T  C02@T  C03@T  C04@T  C05@T  C06@T  C07@T  \\\n",
       "0      ENSG00000000003   518     45     32     51     46     36     31     43   \n",
       "1      ENSG00000000005  2479     22      3     11      0      0      4      9   \n",
       "2      ENSG00000000419   321    193    214    241    158    159    206    198   \n",
       "3      ENSG00000000457   549    144    144    179    125     91    138    125   \n",
       "4      ENSG00000000460   150     25     32     49     13      9     22     21   \n",
       "...                ...   ...    ...    ...    ...    ...    ...    ...    ...   \n",
       "58228  ENSG00000284592     1      0      0      0      0      0      0      0   \n",
       "58229  ENSG00000284594     7      0      0      3      0      0      0      0   \n",
       "58230  ENSG00000284595     0      0      0      0      0      0      0      0   \n",
       "58231  ENSG00000284596     0      0      0      0      0      0      0      0   \n",
       "58232  ENSG00000284600     1      0      2      0      0      0      0      0   \n",
       "\n",
       "       C08@T  ...  P38@T  P40@T  P41@T  P42@T  P43@T  P44@T  P45@T  P46@T  \\\n",
       "0         34  ...      0    147     72     67     70     37    106     17   \n",
       "1          3  ...      2     29     28      6     37      2     27     21   \n",
       "2        134  ...      4    435    287    316    186    230    261     13   \n",
       "3        109  ...      3    250    197    253    159    204    240     97   \n",
       "4         32  ...      4     72     31     47     48     35     55     19   \n",
       "...      ...  ...    ...    ...    ...    ...    ...    ...    ...    ...   \n",
       "58228      1  ...      0      0      0      0      0      0      0      0   \n",
       "58229      1  ...      0      0      0      6      1      4      5      0   \n",
       "58230      0  ...      0      0      0      0      0      0      0      0   \n",
       "58231      0  ...      0      0      0      0      0      0      0      0   \n",
       "58232      2  ...      1      0      0      0      0      0      0      0   \n",
       "\n",
       "       P47@T  P48@T  \n",
       "0         51     66  \n",
       "1          3      1  \n",
       "2        203    253  \n",
       "3         94    173  \n",
       "4         29     43  \n",
       "...      ...    ...  \n",
       "58228      0      0  \n",
       "58229      1      0  \n",
       "58230      0      0  \n",
       "58231      0      0  \n",
       "58232      0      0  \n",
       "\n",
       "[58233 rows x 85 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GSE202745 = pd.read_table(\"GEO data/GSE202745_exp3105-x2-switched-RawCountsTable.txt\")\n",
    "GSE202745 = pd.concat([GSE202745.GeneID, GSE202745.iloc[:,2:86]], axis=1)\n",
    "new_columnnames =  [\"GeneID\"] + GSE202745.iloc[:,1:85].columns.str.extract(r'(\\w{1,3}@T(?=@))')[0].tolist()\n",
    "GSE202745.columns = new_columnnames\n",
    "GSE202745"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GEO combination"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>Pre-S12</th>\n",
       "      <th>Pre-S13</th>\n",
       "      <th>Pre-S2</th>\n",
       "      <th>Pre-S3</th>\n",
       "      <th>Pre-S4</th>\n",
       "      <th>Pre-S5</th>\n",
       "      <th>Pre-S6</th>\n",
       "      <th>Pre-S7</th>\n",
       "      <th>Pre-S8</th>\n",
       "      <th>Pre-S9</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000187634</td>\n",
       "      <td>72</td>\n",
       "      <td>177</td>\n",
       "      <td>66</td>\n",
       "      <td>105</td>\n",
       "      <td>54</td>\n",
       "      <td>46</td>\n",
       "      <td>25</td>\n",
       "      <td>65</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>12</td>\n",
       "      <td>17</td>\n",
       "      <td>3</td>\n",
       "      <td>7</td>\n",
       "      <td>14</td>\n",
       "      <td>142</td>\n",
       "      <td>9</td>\n",
       "      <td>41</td>\n",
       "      <td>116</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000188976</td>\n",
       "      <td>1660</td>\n",
       "      <td>1657</td>\n",
       "      <td>1548</td>\n",
       "      <td>1598</td>\n",
       "      <td>1549</td>\n",
       "      <td>1785</td>\n",
       "      <td>1040</td>\n",
       "      <td>1221</td>\n",
       "      <td>1530</td>\n",
       "      <td>...</td>\n",
       "      <td>544</td>\n",
       "      <td>751</td>\n",
       "      <td>525</td>\n",
       "      <td>305</td>\n",
       "      <td>451</td>\n",
       "      <td>608</td>\n",
       "      <td>722</td>\n",
       "      <td>698</td>\n",
       "      <td>540</td>\n",
       "      <td>543</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000187961</td>\n",
       "      <td>162</td>\n",
       "      <td>219</td>\n",
       "      <td>125</td>\n",
       "      <td>163</td>\n",
       "      <td>94</td>\n",
       "      <td>111</td>\n",
       "      <td>60</td>\n",
       "      <td>79</td>\n",
       "      <td>93</td>\n",
       "      <td>...</td>\n",
       "      <td>32</td>\n",
       "      <td>38</td>\n",
       "      <td>13</td>\n",
       "      <td>26</td>\n",
       "      <td>23</td>\n",
       "      <td>20</td>\n",
       "      <td>56</td>\n",
       "      <td>21</td>\n",
       "      <td>29</td>\n",
       "      <td>41</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000187583</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>172</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000187642</td>\n",
       "      <td>2067</td>\n",
       "      <td>2606</td>\n",
       "      <td>5802</td>\n",
       "      <td>4378</td>\n",
       "      <td>5758</td>\n",
       "      <td>7291</td>\n",
       "      <td>4722</td>\n",
       "      <td>5029</td>\n",
       "      <td>7240</td>\n",
       "      <td>...</td>\n",
       "      <td>1329</td>\n",
       "      <td>1658</td>\n",
       "      <td>1212</td>\n",
       "      <td>825</td>\n",
       "      <td>1296</td>\n",
       "      <td>1739</td>\n",
       "      <td>330</td>\n",
       "      <td>2118</td>\n",
       "      <td>1863</td>\n",
       "      <td>341</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17080</th>\n",
       "      <td>ENSG00000160298</td>\n",
       "      <td>290</td>\n",
       "      <td>306</td>\n",
       "      <td>220</td>\n",
       "      <td>149</td>\n",
       "      <td>108</td>\n",
       "      <td>154</td>\n",
       "      <td>68</td>\n",
       "      <td>93</td>\n",
       "      <td>117</td>\n",
       "      <td>...</td>\n",
       "      <td>22</td>\n",
       "      <td>29</td>\n",
       "      <td>25</td>\n",
       "      <td>26</td>\n",
       "      <td>33</td>\n",
       "      <td>40</td>\n",
       "      <td>43</td>\n",
       "      <td>23</td>\n",
       "      <td>29</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17081</th>\n",
       "      <td>ENSG00000160299</td>\n",
       "      <td>16989</td>\n",
       "      <td>13268</td>\n",
       "      <td>15518</td>\n",
       "      <td>15279</td>\n",
       "      <td>19910</td>\n",
       "      <td>18520</td>\n",
       "      <td>17353</td>\n",
       "      <td>16313</td>\n",
       "      <td>21883</td>\n",
       "      <td>...</td>\n",
       "      <td>4376</td>\n",
       "      <td>5236</td>\n",
       "      <td>5290</td>\n",
       "      <td>2793</td>\n",
       "      <td>2679</td>\n",
       "      <td>2404</td>\n",
       "      <td>4168</td>\n",
       "      <td>4434</td>\n",
       "      <td>2352</td>\n",
       "      <td>4854</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17082</th>\n",
       "      <td>ENSG00000160305</td>\n",
       "      <td>3238</td>\n",
       "      <td>3501</td>\n",
       "      <td>2853</td>\n",
       "      <td>2824</td>\n",
       "      <td>2489</td>\n",
       "      <td>3200</td>\n",
       "      <td>1289</td>\n",
       "      <td>1808</td>\n",
       "      <td>2219</td>\n",
       "      <td>...</td>\n",
       "      <td>583</td>\n",
       "      <td>568</td>\n",
       "      <td>565</td>\n",
       "      <td>502</td>\n",
       "      <td>567</td>\n",
       "      <td>445</td>\n",
       "      <td>619</td>\n",
       "      <td>633</td>\n",
       "      <td>470</td>\n",
       "      <td>527</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17083</th>\n",
       "      <td>ENSG00000160307</td>\n",
       "      <td>56</td>\n",
       "      <td>246</td>\n",
       "      <td>22</td>\n",
       "      <td>245</td>\n",
       "      <td>207</td>\n",
       "      <td>177</td>\n",
       "      <td>190</td>\n",
       "      <td>45</td>\n",
       "      <td>23</td>\n",
       "      <td>...</td>\n",
       "      <td>9</td>\n",
       "      <td>45</td>\n",
       "      <td>44</td>\n",
       "      <td>27</td>\n",
       "      <td>5</td>\n",
       "      <td>11</td>\n",
       "      <td>67</td>\n",
       "      <td>44</td>\n",
       "      <td>3</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17084</th>\n",
       "      <td>ENSG00000160310</td>\n",
       "      <td>2144</td>\n",
       "      <td>2410</td>\n",
       "      <td>1532</td>\n",
       "      <td>1744</td>\n",
       "      <td>1151</td>\n",
       "      <td>1436</td>\n",
       "      <td>687</td>\n",
       "      <td>997</td>\n",
       "      <td>993</td>\n",
       "      <td>...</td>\n",
       "      <td>562</td>\n",
       "      <td>707</td>\n",
       "      <td>669</td>\n",
       "      <td>477</td>\n",
       "      <td>451</td>\n",
       "      <td>559</td>\n",
       "      <td>1267</td>\n",
       "      <td>659</td>\n",
       "      <td>495</td>\n",
       "      <td>1062</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>17085 rows × 292 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  \\\n",
       "0      ENSG00000187634      72     177      66     105      54      46   \n",
       "1      ENSG00000188976    1660    1657    1548    1598    1549    1785   \n",
       "2      ENSG00000187961     162     219     125     163      94     111   \n",
       "3      ENSG00000187583       1       4       2       7     172       4   \n",
       "4      ENSG00000187642    2067    2606    5802    4378    5758    7291   \n",
       "...                ...     ...     ...     ...     ...     ...     ...   \n",
       "17080  ENSG00000160298     290     306     220     149     108     154   \n",
       "17081  ENSG00000160299   16989   13268   15518   15279   19910   18520   \n",
       "17082  ENSG00000160305    3238    3501    2853    2824    2489    3200   \n",
       "17083  ENSG00000160307      56     246      22     245     207     177   \n",
       "17084  ENSG00000160310    2144    2410    1532    1744    1151    1436   \n",
       "\n",
       "       CDM-07  CDM-08  CDM-09  ...  Pre-S12  Pre-S13  Pre-S2  Pre-S3  Pre-S4  \\\n",
       "0          25      65      14  ...        3       12      17       3       7   \n",
       "1        1040    1221    1530  ...      544      751     525     305     451   \n",
       "2          60      79      93  ...       32       38      13      26      23   \n",
       "3           1       3       1  ...        0        0       0       2       0   \n",
       "4        4722    5029    7240  ...     1329     1658    1212     825    1296   \n",
       "...       ...     ...     ...  ...      ...      ...     ...     ...     ...   \n",
       "17080      68      93     117  ...       22       29      25      26      33   \n",
       "17081   17353   16313   21883  ...     4376     5236    5290    2793    2679   \n",
       "17082    1289    1808    2219  ...      583      568     565     502     567   \n",
       "17083     190      45      23  ...        9       45      44      27       5   \n",
       "17084     687     997     993  ...      562      707     669     477     451   \n",
       "\n",
       "       Pre-S5  Pre-S6  Pre-S7  Pre-S8  Pre-S9  \n",
       "0          14     142       9      41     116  \n",
       "1         608     722     698     540     543  \n",
       "2          20      56      21      29      41  \n",
       "3           0       4       0       0       1  \n",
       "4        1739     330    2118    1863     341  \n",
       "...       ...     ...     ...     ...     ...  \n",
       "17080      40      43      23      29      22  \n",
       "17081    2404    4168    4434    2352    4854  \n",
       "17082     445     619     633     470     527  \n",
       "17083      11      67      44       3      12  \n",
       "17084     559    1267     659     495    1062  \n",
       "\n",
       "[17085 rows x 292 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GEO_muscle = pd.merge(GSE201255, GSE202745, how='inner', on='GeneID')\n",
    "GEO_muscle = pd.merge(GEO_muscle, GSE175861, how='inner', on='GeneID')\n",
    "GEO_muscle = pd.merge(GEO_muscle, GSE140261, how='inner', on='GeneID')\n",
    "GEO_muscle = pd.merge(GEO_muscle, GSE115650, how='inner', on='GeneID')\n",
    "GEO_muscle = pd.merge(GEO_muscle, GSE184951, how='inner', on='GeneID')\n",
    "\n",
    "GEO_muscle"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# GTEx combination"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>GTEX-1117F-0426-SM-5EGHI</th>\n",
       "      <th>GTEX-111CU-2026-SM-5GZZC</th>\n",
       "      <th>GTEX-111FC-0326-SM-5GZZ1</th>\n",
       "      <th>GTEX-111VG-2626-SM-5GZY2</th>\n",
       "      <th>GTEX-111YS-2326-SM-5987L</th>\n",
       "      <th>GTEX-1122O-2426-SM-5GIDN</th>\n",
       "      <th>GTEX-1128S-2426-SM-5H11B</th>\n",
       "      <th>GTEX-113JC-2726-SM-5EGIS</th>\n",
       "      <th>GTEX-117XS-2526-SM-5H11G</th>\n",
       "      <th>...</th>\n",
       "      <th>GTEX-ZY6K-2026-SM-5GZXQ</th>\n",
       "      <th>GTEX-ZYFC-0526-SM-5GIDF</th>\n",
       "      <th>GTEX-ZYFD-0326-SM-5NQ8I</th>\n",
       "      <th>GTEX-ZYFG-2426-SM-5GIE8</th>\n",
       "      <th>GTEX-ZYT6-1626-SM-5E45R</th>\n",
       "      <th>GTEX-ZYW4-0526-SM-5GZZ5</th>\n",
       "      <th>GTEX-ZYY3-0526-SM-5E45G</th>\n",
       "      <th>GTEX-ZZ64-1526-SM-5E43K</th>\n",
       "      <th>GTEX-ZZPT-0626-SM-5GZXT</th>\n",
       "      <th>GTEX-ZZPU-2626-SM-5E45Y</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000223972</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000227232</td>\n",
       "      <td>109</td>\n",
       "      <td>40</td>\n",
       "      <td>52</td>\n",
       "      <td>19</td>\n",
       "      <td>29</td>\n",
       "      <td>64</td>\n",
       "      <td>66</td>\n",
       "      <td>33</td>\n",
       "      <td>38</td>\n",
       "      <td>...</td>\n",
       "      <td>223</td>\n",
       "      <td>69</td>\n",
       "      <td>32</td>\n",
       "      <td>47</td>\n",
       "      <td>27</td>\n",
       "      <td>44</td>\n",
       "      <td>65</td>\n",
       "      <td>74</td>\n",
       "      <td>99</td>\n",
       "      <td>34</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000237613</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56195</th>\n",
       "      <td>ENSG00000198695</td>\n",
       "      <td>164596</td>\n",
       "      <td>271981</td>\n",
       "      <td>104807</td>\n",
       "      <td>153177</td>\n",
       "      <td>185456</td>\n",
       "      <td>199394</td>\n",
       "      <td>445293</td>\n",
       "      <td>129277</td>\n",
       "      <td>281196</td>\n",
       "      <td>...</td>\n",
       "      <td>151860</td>\n",
       "      <td>204304</td>\n",
       "      <td>108419</td>\n",
       "      <td>365195</td>\n",
       "      <td>133850</td>\n",
       "      <td>247638</td>\n",
       "      <td>119170</td>\n",
       "      <td>294986</td>\n",
       "      <td>37886</td>\n",
       "      <td>303816</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56196</th>\n",
       "      <td>ENSG00000210194</td>\n",
       "      <td>65</td>\n",
       "      <td>120</td>\n",
       "      <td>41</td>\n",
       "      <td>67</td>\n",
       "      <td>85</td>\n",
       "      <td>86</td>\n",
       "      <td>139</td>\n",
       "      <td>46</td>\n",
       "      <td>109</td>\n",
       "      <td>...</td>\n",
       "      <td>49</td>\n",
       "      <td>90</td>\n",
       "      <td>35</td>\n",
       "      <td>189</td>\n",
       "      <td>17</td>\n",
       "      <td>102</td>\n",
       "      <td>45</td>\n",
       "      <td>151</td>\n",
       "      <td>8</td>\n",
       "      <td>120</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56197</th>\n",
       "      <td>ENSG00000198727</td>\n",
       "      <td>638209</td>\n",
       "      <td>1114514</td>\n",
       "      <td>1318175</td>\n",
       "      <td>650782</td>\n",
       "      <td>922519</td>\n",
       "      <td>921817</td>\n",
       "      <td>1814597</td>\n",
       "      <td>900959</td>\n",
       "      <td>1082032</td>\n",
       "      <td>...</td>\n",
       "      <td>1304160</td>\n",
       "      <td>814191</td>\n",
       "      <td>902797</td>\n",
       "      <td>1181827</td>\n",
       "      <td>1237537</td>\n",
       "      <td>644574</td>\n",
       "      <td>1027530</td>\n",
       "      <td>1084657</td>\n",
       "      <td>680051</td>\n",
       "      <td>1231647</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56198</th>\n",
       "      <td>ENSG00000210195</td>\n",
       "      <td>9</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>224</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>7</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>93</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56199</th>\n",
       "      <td>ENSG00000210196</td>\n",
       "      <td>9</td>\n",
       "      <td>4</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>5</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>57</td>\n",
       "      <td>276</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>56200 rows × 804 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  GTEX-1117F-0426-SM-5EGHI  GTEX-111CU-2026-SM-5GZZC  \\\n",
       "0      ENSG00000223972                         0                         0   \n",
       "1      ENSG00000227232                       109                        40   \n",
       "2      ENSG00000278267                         0                         0   \n",
       "3      ENSG00000243485                         0                         0   \n",
       "4      ENSG00000237613                         0                         0   \n",
       "...                ...                       ...                       ...   \n",
       "56195  ENSG00000198695                    164596                    271981   \n",
       "56196  ENSG00000210194                        65                       120   \n",
       "56197  ENSG00000198727                    638209                   1114514   \n",
       "56198  ENSG00000210195                         9                         2   \n",
       "56199  ENSG00000210196                         9                         4   \n",
       "\n",
       "       GTEX-111FC-0326-SM-5GZZ1  GTEX-111VG-2626-SM-5GZY2  \\\n",
       "0                             1                         0   \n",
       "1                            52                        19   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             1                         1   \n",
       "...                         ...                       ...   \n",
       "56195                    104807                    153177   \n",
       "56196                        41                        67   \n",
       "56197                   1318175                    650782   \n",
       "56198                         4                         1   \n",
       "56199                         6                         2   \n",
       "\n",
       "       GTEX-111YS-2326-SM-5987L  GTEX-1122O-2426-SM-5GIDN  \\\n",
       "0                             0                         0   \n",
       "1                            29                        64   \n",
       "2                             0                         0   \n",
       "3                             0                         0   \n",
       "4                             2                         1   \n",
       "...                         ...                       ...   \n",
       "56195                    185456                    199394   \n",
       "56196                        85                        86   \n",
       "56197                    922519                    921817   \n",
       "56198                         4                         1   \n",
       "56199                         4                         3   \n",
       "\n",
       "       GTEX-1128S-2426-SM-5H11B  GTEX-113JC-2726-SM-5EGIS  \\\n",
       "0                             0                         0   \n",
       "1                            66                        33   \n",
       "2                             0                         0   \n",
       "3                             0                         1   \n",
       "4                             0                         0   \n",
       "...                         ...                       ...   \n",
       "56195                    445293                    129277   \n",
       "56196                       139                        46   \n",
       "56197                   1814597                    900959   \n",
       "56198                         7                         1   \n",
       "56199                         5                         3   \n",
       "\n",
       "       GTEX-117XS-2526-SM-5H11G  ...  GTEX-ZY6K-2026-SM-5GZXQ  \\\n",
       "0                             0  ...                        3   \n",
       "1                            38  ...                      223   \n",
       "2                             0  ...                        0   \n",
       "3                             1  ...                        1   \n",
       "4                             0  ...                        1   \n",
       "...                         ...  ...                      ...   \n",
       "56195                    281196  ...                   151860   \n",
       "56196                       109  ...                       49   \n",
       "56197                   1082032  ...                  1304160   \n",
       "56198                         0  ...                        3   \n",
       "56199                         3  ...                        6   \n",
       "\n",
       "       GTEX-ZYFC-0526-SM-5GIDF  GTEX-ZYFD-0326-SM-5NQ8I  \\\n",
       "0                            1                        0   \n",
       "1                           69                       32   \n",
       "2                            0                        0   \n",
       "3                            1                        0   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   204304                   108419   \n",
       "56196                       90                       35   \n",
       "56197                   814191                   902797   \n",
       "56198                      224                        7   \n",
       "56199                        2                       57   \n",
       "\n",
       "       GTEX-ZYFG-2426-SM-5GIE8  GTEX-ZYT6-1626-SM-5E45R  \\\n",
       "0                            0                        0   \n",
       "1                           47                       27   \n",
       "2                            0                        0   \n",
       "3                            0                        0   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   365195                   133850   \n",
       "56196                      189                       17   \n",
       "56197                  1181827                  1237537   \n",
       "56198                        7                        1   \n",
       "56199                      276                        1   \n",
       "\n",
       "       GTEX-ZYW4-0526-SM-5GZZ5  GTEX-ZYY3-0526-SM-5E45G  \\\n",
       "0                            0                        0   \n",
       "1                           44                       65   \n",
       "2                            0                        0   \n",
       "3                            0                        1   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   247638                   119170   \n",
       "56196                      102                       45   \n",
       "56197                   644574                  1027530   \n",
       "56198                        4                        7   \n",
       "56199                        4                        3   \n",
       "\n",
       "       GTEX-ZZ64-1526-SM-5E43K  GTEX-ZZPT-0626-SM-5GZXT  \\\n",
       "0                            0                        1   \n",
       "1                           74                       99   \n",
       "2                            0                        0   \n",
       "3                            0                        2   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "56195                   294986                    37886   \n",
       "56196                      151                        8   \n",
       "56197                  1084657                   680051   \n",
       "56198                        6                        1   \n",
       "56199                        4                        1   \n",
       "\n",
       "       GTEX-ZZPU-2626-SM-5E45Y  \n",
       "0                            1  \n",
       "1                           34  \n",
       "2                            0  \n",
       "3                            0  \n",
       "4                            0  \n",
       "...                        ...  \n",
       "56195                   303816  \n",
       "56196                      120  \n",
       "56197                  1231647  \n",
       "56198                       93  \n",
       "56199                        9  \n",
       "\n",
       "[56200 rows x 804 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GTEx_muscle = pd.read_table(\"GTEx data/gene_reads_muscle_skeletal.txt\")\n",
    "GTEx_muscle.GeneID = GTEx_muscle.GeneID.str.extract(r'(ENSG.+(?=\\.))')\n",
    "GTEx_muscle.drop(['GeneSymbol'], axis=1, inplace=True)\n",
    "GTEx_muscle"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Helsinki combination"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>0_FM1812</th>\n",
       "      <th>0_FM22</th>\n",
       "      <th>0_FM2670</th>\n",
       "      <th>0_FM3310</th>\n",
       "      <th>0_FM3311</th>\n",
       "      <th>0_FM3591</th>\n",
       "      <th>0_FM3894</th>\n",
       "      <th>0_FM3901</th>\n",
       "      <th>0_FM4021</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000223972</td>\n",
       "      <td>1</td>\n",
       "      <td>12</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000227232</td>\n",
       "      <td>122</td>\n",
       "      <td>229</td>\n",
       "      <td>139</td>\n",
       "      <td>74</td>\n",
       "      <td>153</td>\n",
       "      <td>95</td>\n",
       "      <td>117</td>\n",
       "      <td>165</td>\n",
       "      <td>99</td>\n",
       "      <td>...</td>\n",
       "      <td>207.0</td>\n",
       "      <td>281.0</td>\n",
       "      <td>454.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>449.0</td>\n",
       "      <td>207.0</td>\n",
       "      <td>695.0</td>\n",
       "      <td>572.0</td>\n",
       "      <td>881.0</td>\n",
       "      <td>708.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267</td>\n",
       "      <td>22</td>\n",
       "      <td>28</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>18</td>\n",
       "      <td>12</td>\n",
       "      <td>24</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>19.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>52.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>53.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>34.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485</td>\n",
       "      <td>6</td>\n",
       "      <td>10</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000284332</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61582</th>\n",
       "      <td>ENSG00000276017</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61583</th>\n",
       "      <td>ENSG00000278817</td>\n",
       "      <td>264</td>\n",
       "      <td>186</td>\n",
       "      <td>660</td>\n",
       "      <td>472</td>\n",
       "      <td>748</td>\n",
       "      <td>375</td>\n",
       "      <td>688</td>\n",
       "      <td>313</td>\n",
       "      <td>247</td>\n",
       "      <td>...</td>\n",
       "      <td>747.0</td>\n",
       "      <td>876.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>479.0</td>\n",
       "      <td>250.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>892.0</td>\n",
       "      <td>617.0</td>\n",
       "      <td>927.0</td>\n",
       "      <td>687.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61584</th>\n",
       "      <td>ENSG00000277196</td>\n",
       "      <td>106</td>\n",
       "      <td>59</td>\n",
       "      <td>107</td>\n",
       "      <td>261</td>\n",
       "      <td>231</td>\n",
       "      <td>107</td>\n",
       "      <td>168</td>\n",
       "      <td>90</td>\n",
       "      <td>132</td>\n",
       "      <td>...</td>\n",
       "      <td>147.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>415.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>150.0</td>\n",
       "      <td>305.0</td>\n",
       "      <td>1023.0</td>\n",
       "      <td>429.0</td>\n",
       "      <td>2899.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61585</th>\n",
       "      <td>ENSG00000278625</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61586</th>\n",
       "      <td>ENSG00000277374</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>61587 rows × 128 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  0_FM1812  0_FM22  0_FM2670  0_FM3310  0_FM3311  \\\n",
       "0      ENSG00000223972         1      12         2         7         0   \n",
       "1      ENSG00000227232       122     229       139        74       153   \n",
       "2      ENSG00000278267        22      28         9         8         8   \n",
       "3      ENSG00000243485         6      10         6         2         3   \n",
       "4      ENSG00000284332         0       0         0         0         0   \n",
       "...                ...       ...     ...       ...       ...       ...   \n",
       "61582  ENSG00000276017         0       0         0         0         0   \n",
       "61583  ENSG00000278817       264     186       660       472       748   \n",
       "61584  ENSG00000277196       106      59       107       261       231   \n",
       "61585  ENSG00000278625         0       0         0         0         0   \n",
       "61586  ENSG00000277374         0       0         0         0         0   \n",
       "\n",
       "       0_FM3591  0_FM3894  0_FM3901  0_FM4021  ...  9_FM3690_2  9_FM3764  \\\n",
       "0             0         1         2         4  ...         0.0       1.0   \n",
       "1            95       117       165        99  ...       207.0     281.0   \n",
       "2            18        12        24        10  ...        19.0      15.0   \n",
       "3             2         1         0         0  ...         0.0       0.0   \n",
       "4             0         0         0         0  ...         0.0       0.0   \n",
       "...         ...       ...       ...       ...  ...         ...       ...   \n",
       "61582         0         0         0         0  ...         0.0       0.0   \n",
       "61583       375       688       313       247  ...       747.0     876.0   \n",
       "61584       107       168        90       132  ...       147.0     240.0   \n",
       "61585         0         0         0         0  ...         0.0       0.0   \n",
       "61586         0         0         0         0  ...         0.0       0.0   \n",
       "\n",
       "       9_FM3796  9_FM3799  9_FM3800  9_FM3814  9_FM3835  9_HL_VL_AMP08  \\\n",
       "0           8.0       1.0       0.0       1.0       0.0            0.0   \n",
       "1         454.0     263.0     449.0     207.0     695.0          572.0   \n",
       "2          55.0       6.0      52.0      25.0      53.0           40.0   \n",
       "3           1.0       3.0       1.0       0.0       1.0            0.0   \n",
       "4           0.0       0.0       0.0       0.0       0.0            0.0   \n",
       "...         ...       ...       ...       ...       ...            ...   \n",
       "61582       0.0       0.0       0.0       0.0       0.0            0.0   \n",
       "61583     592.0     479.0     250.0     405.0     892.0          617.0   \n",
       "61584     415.0      48.0     405.0     150.0     305.0         1023.0   \n",
       "61585       0.0       0.0       0.0       0.0       0.0            0.0   \n",
       "61586       0.0       0.0       0.0       0.0       0.0            0.0   \n",
       "\n",
       "       9_JE_VL_AMP05  9_KO_AMP09  \n",
       "0                0.0         0.0  \n",
       "1              881.0       708.0  \n",
       "2               56.0        34.0  \n",
       "3                0.0         0.0  \n",
       "4                0.0         0.0  \n",
       "...              ...         ...  \n",
       "61582            0.0         0.0  \n",
       "61583          927.0       687.0  \n",
       "61584          429.0      2899.0  \n",
       "61585            0.0         0.0  \n",
       "61586            0.0         0.0  \n",
       "\n",
       "[61587 rows x 128 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Helsinki_muscle_L = pd.read_csv(\"Helsinki data/merge_L_Helsinki.csv\")\n",
    "# remove non-human samples (cell-line, mouse muscles) from the original merge_L_Helsinki.csv file\n",
    "Meta_Helsinki = pd.read_excel('Meta/RNA-seq integration meta.xlsx', sheet_name='Helsinki')  \n",
    "Helsinki_muscle = pd.concat([ Helsinki_muscle_L['GeneID'], Helsinki_muscle_L[Meta_Helsinki.Sample_id] ], axis=1)\n",
    "Helsinki_muscle.GeneID = Helsinki_muscle.GeneID.str.extract(r'(ENSG.+(?=\\.))')\n",
    "Helsinki_muscle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "Helsinki_muscle.to_csv('Integration data/Helsinki_128_muscles.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# All combination"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000187634</td>\n",
       "      <td>72</td>\n",
       "      <td>177</td>\n",
       "      <td>66</td>\n",
       "      <td>105</td>\n",
       "      <td>54</td>\n",
       "      <td>46</td>\n",
       "      <td>25</td>\n",
       "      <td>65</td>\n",
       "      <td>14</td>\n",
       "      <td>...</td>\n",
       "      <td>8.0</td>\n",
       "      <td>398.0</td>\n",
       "      <td>408.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>687.0</td>\n",
       "      <td>1068.0</td>\n",
       "      <td>584.0</td>\n",
       "      <td>549.0</td>\n",
       "      <td>15.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000188976</td>\n",
       "      <td>1660</td>\n",
       "      <td>1657</td>\n",
       "      <td>1548</td>\n",
       "      <td>1598</td>\n",
       "      <td>1549</td>\n",
       "      <td>1785</td>\n",
       "      <td>1040</td>\n",
       "      <td>1221</td>\n",
       "      <td>1530</td>\n",
       "      <td>...</td>\n",
       "      <td>3596.0</td>\n",
       "      <td>3651.0</td>\n",
       "      <td>4258.0</td>\n",
       "      <td>3055.0</td>\n",
       "      <td>4565.0</td>\n",
       "      <td>1789.0</td>\n",
       "      <td>4180.0</td>\n",
       "      <td>5231.0</td>\n",
       "      <td>8196.0</td>\n",
       "      <td>8402.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000187961</td>\n",
       "      <td>162</td>\n",
       "      <td>219</td>\n",
       "      <td>125</td>\n",
       "      <td>163</td>\n",
       "      <td>94</td>\n",
       "      <td>111</td>\n",
       "      <td>60</td>\n",
       "      <td>79</td>\n",
       "      <td>93</td>\n",
       "      <td>...</td>\n",
       "      <td>111.0</td>\n",
       "      <td>229.0</td>\n",
       "      <td>391.0</td>\n",
       "      <td>135.0</td>\n",
       "      <td>192.0</td>\n",
       "      <td>130.0</td>\n",
       "      <td>319.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>445.0</td>\n",
       "      <td>267.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000187583</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>172</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>24.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>19.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000187642</td>\n",
       "      <td>2067</td>\n",
       "      <td>2606</td>\n",
       "      <td>5802</td>\n",
       "      <td>4378</td>\n",
       "      <td>5758</td>\n",
       "      <td>7291</td>\n",
       "      <td>4722</td>\n",
       "      <td>5029</td>\n",
       "      <td>7240</td>\n",
       "      <td>...</td>\n",
       "      <td>26682.0</td>\n",
       "      <td>12082.0</td>\n",
       "      <td>5923.0</td>\n",
       "      <td>14166.0</td>\n",
       "      <td>13120.0</td>\n",
       "      <td>597.0</td>\n",
       "      <td>4478.0</td>\n",
       "      <td>6682.0</td>\n",
       "      <td>4993.0</td>\n",
       "      <td>4021.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16948</th>\n",
       "      <td>ENSG00000160298</td>\n",
       "      <td>290</td>\n",
       "      <td>306</td>\n",
       "      <td>220</td>\n",
       "      <td>149</td>\n",
       "      <td>108</td>\n",
       "      <td>154</td>\n",
       "      <td>68</td>\n",
       "      <td>93</td>\n",
       "      <td>117</td>\n",
       "      <td>...</td>\n",
       "      <td>57.0</td>\n",
       "      <td>144.0</td>\n",
       "      <td>229.0</td>\n",
       "      <td>80.0</td>\n",
       "      <td>134.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>303.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>225.0</td>\n",
       "      <td>122.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16949</th>\n",
       "      <td>ENSG00000160299</td>\n",
       "      <td>16989</td>\n",
       "      <td>13268</td>\n",
       "      <td>15518</td>\n",
       "      <td>15279</td>\n",
       "      <td>19910</td>\n",
       "      <td>18520</td>\n",
       "      <td>17353</td>\n",
       "      <td>16313</td>\n",
       "      <td>21883</td>\n",
       "      <td>...</td>\n",
       "      <td>18572.0</td>\n",
       "      <td>11005.0</td>\n",
       "      <td>8842.0</td>\n",
       "      <td>15252.0</td>\n",
       "      <td>19719.0</td>\n",
       "      <td>3982.0</td>\n",
       "      <td>10027.0</td>\n",
       "      <td>32484.0</td>\n",
       "      <td>17641.0</td>\n",
       "      <td>39311.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16950</th>\n",
       "      <td>ENSG00000160305</td>\n",
       "      <td>3238</td>\n",
       "      <td>3501</td>\n",
       "      <td>2853</td>\n",
       "      <td>2824</td>\n",
       "      <td>2489</td>\n",
       "      <td>3200</td>\n",
       "      <td>1289</td>\n",
       "      <td>1808</td>\n",
       "      <td>2219</td>\n",
       "      <td>...</td>\n",
       "      <td>1288.0</td>\n",
       "      <td>1329.0</td>\n",
       "      <td>2803.0</td>\n",
       "      <td>1851.0</td>\n",
       "      <td>2316.0</td>\n",
       "      <td>859.0</td>\n",
       "      <td>2701.0</td>\n",
       "      <td>2914.0</td>\n",
       "      <td>2095.0</td>\n",
       "      <td>3156.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16951</th>\n",
       "      <td>ENSG00000160307</td>\n",
       "      <td>56</td>\n",
       "      <td>246</td>\n",
       "      <td>22</td>\n",
       "      <td>245</td>\n",
       "      <td>207</td>\n",
       "      <td>177</td>\n",
       "      <td>190</td>\n",
       "      <td>45</td>\n",
       "      <td>23</td>\n",
       "      <td>...</td>\n",
       "      <td>37.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>11200.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>419.0</td>\n",
       "      <td>1176.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>13.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16952</th>\n",
       "      <td>ENSG00000160310</td>\n",
       "      <td>2144</td>\n",
       "      <td>2410</td>\n",
       "      <td>1532</td>\n",
       "      <td>1744</td>\n",
       "      <td>1151</td>\n",
       "      <td>1436</td>\n",
       "      <td>687</td>\n",
       "      <td>997</td>\n",
       "      <td>993</td>\n",
       "      <td>...</td>\n",
       "      <td>1087.0</td>\n",
       "      <td>2779.0</td>\n",
       "      <td>8156.0</td>\n",
       "      <td>900.0</td>\n",
       "      <td>1091.0</td>\n",
       "      <td>1505.0</td>\n",
       "      <td>4738.0</td>\n",
       "      <td>1027.0</td>\n",
       "      <td>1761.0</td>\n",
       "      <td>913.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>16953 rows × 1222 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                GeneID  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  \\\n",
       "0      ENSG00000187634      72     177      66     105      54      46   \n",
       "1      ENSG00000188976    1660    1657    1548    1598    1549    1785   \n",
       "2      ENSG00000187961     162     219     125     163      94     111   \n",
       "3      ENSG00000187583       1       4       2       7     172       4   \n",
       "4      ENSG00000187642    2067    2606    5802    4378    5758    7291   \n",
       "...                ...     ...     ...     ...     ...     ...     ...   \n",
       "16948  ENSG00000160298     290     306     220     149     108     154   \n",
       "16949  ENSG00000160299   16989   13268   15518   15279   19910   18520   \n",
       "16950  ENSG00000160305    3238    3501    2853    2824    2489    3200   \n",
       "16951  ENSG00000160307      56     246      22     245     207     177   \n",
       "16952  ENSG00000160310    2144    2410    1532    1744    1151    1436   \n",
       "\n",
       "       CDM-07  CDM-08  CDM-09  ...  9_FM3690_2  9_FM3764  9_FM3796  9_FM3799  \\\n",
       "0          25      65      14  ...         8.0     398.0     408.0       8.0   \n",
       "1        1040    1221    1530  ...      3596.0    3651.0    4258.0    3055.0   \n",
       "2          60      79      93  ...       111.0     229.0     391.0     135.0   \n",
       "3           1       3       1  ...        24.0      40.0      40.0       9.0   \n",
       "4        4722    5029    7240  ...     26682.0   12082.0    5923.0   14166.0   \n",
       "...       ...     ...     ...  ...         ...       ...       ...       ...   \n",
       "16948      68      93     117  ...        57.0     144.0     229.0      80.0   \n",
       "16949   17353   16313   21883  ...     18572.0   11005.0    8842.0   15252.0   \n",
       "16950    1289    1808    2219  ...      1288.0    1329.0    2803.0    1851.0   \n",
       "16951     190      45      23  ...        37.0      69.0   11200.0       5.0   \n",
       "16952     687     997     993  ...      1087.0    2779.0    8156.0     900.0   \n",
       "\n",
       "       9_FM3800  9_FM3814  9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  9_KO_AMP09  \n",
       "0          14.0     687.0    1068.0          584.0          549.0        15.0  \n",
       "1        4565.0    1789.0    4180.0         5231.0         8196.0      8402.0  \n",
       "2         192.0     130.0     319.0          330.0          445.0       267.0  \n",
       "3          11.0       7.0      19.0            9.0           32.0        19.0  \n",
       "4       13120.0     597.0    4478.0         6682.0         4993.0      4021.0  \n",
       "...         ...       ...       ...            ...            ...         ...  \n",
       "16948     134.0      83.0     303.0          195.0          225.0       122.0  \n",
       "16949   19719.0    3982.0   10027.0        32484.0        17641.0     39311.0  \n",
       "16950    2316.0     859.0    2701.0         2914.0         2095.0      3156.0  \n",
       "16951       6.0     419.0    1176.0            4.0           47.0        13.0  \n",
       "16952    1091.0    1505.0    4738.0         1027.0         1761.0       913.0  \n",
       "\n",
       "[16953 rows x 1222 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "All_muscle = pd.merge(GEO_muscle, GTEx_muscle, how='inner', on='GeneID')\n",
    "All_muscle = pd.merge(All_muscle, Helsinki_muscle, how='inner', on='GeneID')\n",
    "All_muscle"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Filter those genes > 0 in every samples \n",
    "- To remove those genes with count inflation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000188976</td>\n",
       "      <td>1660</td>\n",
       "      <td>1657</td>\n",
       "      <td>1548</td>\n",
       "      <td>1598</td>\n",
       "      <td>1549</td>\n",
       "      <td>1785</td>\n",
       "      <td>1040</td>\n",
       "      <td>1221</td>\n",
       "      <td>1530</td>\n",
       "      <td>...</td>\n",
       "      <td>3596</td>\n",
       "      <td>3651</td>\n",
       "      <td>4258</td>\n",
       "      <td>3055</td>\n",
       "      <td>4565</td>\n",
       "      <td>1789</td>\n",
       "      <td>4180</td>\n",
       "      <td>5231</td>\n",
       "      <td>8196</td>\n",
       "      <td>8402</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000187642</td>\n",
       "      <td>2067</td>\n",
       "      <td>2606</td>\n",
       "      <td>5802</td>\n",
       "      <td>4378</td>\n",
       "      <td>5758</td>\n",
       "      <td>7291</td>\n",
       "      <td>4722</td>\n",
       "      <td>5029</td>\n",
       "      <td>7240</td>\n",
       "      <td>...</td>\n",
       "      <td>26682</td>\n",
       "      <td>12082</td>\n",
       "      <td>5923</td>\n",
       "      <td>14166</td>\n",
       "      <td>13120</td>\n",
       "      <td>597</td>\n",
       "      <td>4478</td>\n",
       "      <td>6682</td>\n",
       "      <td>4993</td>\n",
       "      <td>4021</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000188157</td>\n",
       "      <td>1437</td>\n",
       "      <td>2687</td>\n",
       "      <td>1852</td>\n",
       "      <td>1500</td>\n",
       "      <td>1103</td>\n",
       "      <td>1049</td>\n",
       "      <td>570</td>\n",
       "      <td>928</td>\n",
       "      <td>694</td>\n",
       "      <td>...</td>\n",
       "      <td>555</td>\n",
       "      <td>1994</td>\n",
       "      <td>2891</td>\n",
       "      <td>483</td>\n",
       "      <td>525</td>\n",
       "      <td>889</td>\n",
       "      <td>1930</td>\n",
       "      <td>719</td>\n",
       "      <td>1839</td>\n",
       "      <td>746</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000078808</td>\n",
       "      <td>1230</td>\n",
       "      <td>1760</td>\n",
       "      <td>1567</td>\n",
       "      <td>1860</td>\n",
       "      <td>1262</td>\n",
       "      <td>1654</td>\n",
       "      <td>1035</td>\n",
       "      <td>1109</td>\n",
       "      <td>1488</td>\n",
       "      <td>...</td>\n",
       "      <td>3418</td>\n",
       "      <td>5465</td>\n",
       "      <td>10102</td>\n",
       "      <td>3924</td>\n",
       "      <td>4388</td>\n",
       "      <td>3189</td>\n",
       "      <td>6184</td>\n",
       "      <td>4797</td>\n",
       "      <td>6962</td>\n",
       "      <td>6711</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000160087</td>\n",
       "      <td>796</td>\n",
       "      <td>896</td>\n",
       "      <td>680</td>\n",
       "      <td>786</td>\n",
       "      <td>748</td>\n",
       "      <td>839</td>\n",
       "      <td>443</td>\n",
       "      <td>576</td>\n",
       "      <td>732</td>\n",
       "      <td>...</td>\n",
       "      <td>1453</td>\n",
       "      <td>1935</td>\n",
       "      <td>2553</td>\n",
       "      <td>1526</td>\n",
       "      <td>1579</td>\n",
       "      <td>1066</td>\n",
       "      <td>2029</td>\n",
       "      <td>1703</td>\n",
       "      <td>2905</td>\n",
       "      <td>2191</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9227</th>\n",
       "      <td>ENSG00000160294</td>\n",
       "      <td>3771</td>\n",
       "      <td>4043</td>\n",
       "      <td>3610</td>\n",
       "      <td>3821</td>\n",
       "      <td>3358</td>\n",
       "      <td>4222</td>\n",
       "      <td>2243</td>\n",
       "      <td>2785</td>\n",
       "      <td>3555</td>\n",
       "      <td>...</td>\n",
       "      <td>4292</td>\n",
       "      <td>3556</td>\n",
       "      <td>5578</td>\n",
       "      <td>3769</td>\n",
       "      <td>5033</td>\n",
       "      <td>1902</td>\n",
       "      <td>4685</td>\n",
       "      <td>5744</td>\n",
       "      <td>6454</td>\n",
       "      <td>6584</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9228</th>\n",
       "      <td>ENSG00000182362</td>\n",
       "      <td>206</td>\n",
       "      <td>201</td>\n",
       "      <td>207</td>\n",
       "      <td>231</td>\n",
       "      <td>135</td>\n",
       "      <td>176</td>\n",
       "      <td>119</td>\n",
       "      <td>109</td>\n",
       "      <td>197</td>\n",
       "      <td>...</td>\n",
       "      <td>351</td>\n",
       "      <td>513</td>\n",
       "      <td>635</td>\n",
       "      <td>250</td>\n",
       "      <td>279</td>\n",
       "      <td>190</td>\n",
       "      <td>532</td>\n",
       "      <td>315</td>\n",
       "      <td>622</td>\n",
       "      <td>530</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9229</th>\n",
       "      <td>ENSG00000160299</td>\n",
       "      <td>16989</td>\n",
       "      <td>13268</td>\n",
       "      <td>15518</td>\n",
       "      <td>15279</td>\n",
       "      <td>19910</td>\n",
       "      <td>18520</td>\n",
       "      <td>17353</td>\n",
       "      <td>16313</td>\n",
       "      <td>21883</td>\n",
       "      <td>...</td>\n",
       "      <td>18572</td>\n",
       "      <td>11005</td>\n",
       "      <td>8842</td>\n",
       "      <td>15252</td>\n",
       "      <td>19719</td>\n",
       "      <td>3982</td>\n",
       "      <td>10027</td>\n",
       "      <td>32484</td>\n",
       "      <td>17641</td>\n",
       "      <td>39311</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9230</th>\n",
       "      <td>ENSG00000160305</td>\n",
       "      <td>3238</td>\n",
       "      <td>3501</td>\n",
       "      <td>2853</td>\n",
       "      <td>2824</td>\n",
       "      <td>2489</td>\n",
       "      <td>3200</td>\n",
       "      <td>1289</td>\n",
       "      <td>1808</td>\n",
       "      <td>2219</td>\n",
       "      <td>...</td>\n",
       "      <td>1288</td>\n",
       "      <td>1329</td>\n",
       "      <td>2803</td>\n",
       "      <td>1851</td>\n",
       "      <td>2316</td>\n",
       "      <td>859</td>\n",
       "      <td>2701</td>\n",
       "      <td>2914</td>\n",
       "      <td>2095</td>\n",
       "      <td>3156</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9231</th>\n",
       "      <td>ENSG00000160310</td>\n",
       "      <td>2144</td>\n",
       "      <td>2410</td>\n",
       "      <td>1532</td>\n",
       "      <td>1744</td>\n",
       "      <td>1151</td>\n",
       "      <td>1436</td>\n",
       "      <td>687</td>\n",
       "      <td>997</td>\n",
       "      <td>993</td>\n",
       "      <td>...</td>\n",
       "      <td>1087</td>\n",
       "      <td>2779</td>\n",
       "      <td>8156</td>\n",
       "      <td>900</td>\n",
       "      <td>1091</td>\n",
       "      <td>1505</td>\n",
       "      <td>4738</td>\n",
       "      <td>1027</td>\n",
       "      <td>1761</td>\n",
       "      <td>913</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9232 rows × 1222 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               GeneID  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  CDM-07  \\\n",
       "0     ENSG00000188976    1660    1657    1548    1598    1549    1785    1040   \n",
       "1     ENSG00000187642    2067    2606    5802    4378    5758    7291    4722   \n",
       "2     ENSG00000188157    1437    2687    1852    1500    1103    1049     570   \n",
       "3     ENSG00000078808    1230    1760    1567    1860    1262    1654    1035   \n",
       "4     ENSG00000160087     796     896     680     786     748     839     443   \n",
       "...               ...     ...     ...     ...     ...     ...     ...     ...   \n",
       "9227  ENSG00000160294    3771    4043    3610    3821    3358    4222    2243   \n",
       "9228  ENSG00000182362     206     201     207     231     135     176     119   \n",
       "9229  ENSG00000160299   16989   13268   15518   15279   19910   18520   17353   \n",
       "9230  ENSG00000160305    3238    3501    2853    2824    2489    3200    1289   \n",
       "9231  ENSG00000160310    2144    2410    1532    1744    1151    1436     687   \n",
       "\n",
       "      CDM-08  CDM-09  ...  9_FM3690_2  9_FM3764  9_FM3796  9_FM3799  9_FM3800  \\\n",
       "0       1221    1530  ...        3596      3651      4258      3055      4565   \n",
       "1       5029    7240  ...       26682     12082      5923     14166     13120   \n",
       "2        928     694  ...         555      1994      2891       483       525   \n",
       "3       1109    1488  ...        3418      5465     10102      3924      4388   \n",
       "4        576     732  ...        1453      1935      2553      1526      1579   \n",
       "...      ...     ...  ...         ...       ...       ...       ...       ...   \n",
       "9227    2785    3555  ...        4292      3556      5578      3769      5033   \n",
       "9228     109     197  ...         351       513       635       250       279   \n",
       "9229   16313   21883  ...       18572     11005      8842     15252     19719   \n",
       "9230    1808    2219  ...        1288      1329      2803      1851      2316   \n",
       "9231     997     993  ...        1087      2779      8156       900      1091   \n",
       "\n",
       "      9_FM3814  9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  9_KO_AMP09  \n",
       "0         1789      4180           5231           8196        8402  \n",
       "1          597      4478           6682           4993        4021  \n",
       "2          889      1930            719           1839         746  \n",
       "3         3189      6184           4797           6962        6711  \n",
       "4         1066      2029           1703           2905        2191  \n",
       "...        ...       ...            ...            ...         ...  \n",
       "9227      1902      4685           5744           6454        6584  \n",
       "9228       190       532            315            622         530  \n",
       "9229      3982     10027          32484          17641       39311  \n",
       "9230       859      2701           2914           2095        3156  \n",
       "9231      1505      4738           1027           1761         913  \n",
       "\n",
       "[9232 rows x 1222 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "All_muscle = All_muscle.dropna(how='any').set_index('GeneID').astype(int) #remove one raw contains some NA\n",
    "All_muscle = All_muscle[(All_muscle > 0).all(axis=1)] \n",
    "All_muscle = All_muscle.reset_index()\n",
    "All_muscle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "All_muscle.to_csv('Integration data/All_muscle_L_raw_GeneID.csv', index=False)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Gene symbal dictionary\n",
    "- Change the first column Ensembl IDs to Gene symbols"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# load dictionary\n",
    "GeneID_anno = pd.read_csv(\"Meta/Annotation_dict_from_GTEx.csv\") # this file is extracted from the GTEx data\n",
    "Genelist = GeneID_anno[GeneID_anno.GeneID.isin(All_muscle.GeneID)].GeneID.tolist()\n",
    "GeneID_dict = dict(zip(GeneID_anno.GeneID, GeneID_anno.GeneSymbol))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "      <th>Symbol</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000188976</td>\n",
       "      <td>1660</td>\n",
       "      <td>1657</td>\n",
       "      <td>1548</td>\n",
       "      <td>1598</td>\n",
       "      <td>1549</td>\n",
       "      <td>1785</td>\n",
       "      <td>1040</td>\n",
       "      <td>1221</td>\n",
       "      <td>1530</td>\n",
       "      <td>...</td>\n",
       "      <td>3651</td>\n",
       "      <td>4258</td>\n",
       "      <td>3055</td>\n",
       "      <td>4565</td>\n",
       "      <td>1789</td>\n",
       "      <td>4180</td>\n",
       "      <td>5231</td>\n",
       "      <td>8196</td>\n",
       "      <td>8402</td>\n",
       "      <td>NOC2L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000187642</td>\n",
       "      <td>2067</td>\n",
       "      <td>2606</td>\n",
       "      <td>5802</td>\n",
       "      <td>4378</td>\n",
       "      <td>5758</td>\n",
       "      <td>7291</td>\n",
       "      <td>4722</td>\n",
       "      <td>5029</td>\n",
       "      <td>7240</td>\n",
       "      <td>...</td>\n",
       "      <td>12082</td>\n",
       "      <td>5923</td>\n",
       "      <td>14166</td>\n",
       "      <td>13120</td>\n",
       "      <td>597</td>\n",
       "      <td>4478</td>\n",
       "      <td>6682</td>\n",
       "      <td>4993</td>\n",
       "      <td>4021</td>\n",
       "      <td>PERM1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000188157</td>\n",
       "      <td>1437</td>\n",
       "      <td>2687</td>\n",
       "      <td>1852</td>\n",
       "      <td>1500</td>\n",
       "      <td>1103</td>\n",
       "      <td>1049</td>\n",
       "      <td>570</td>\n",
       "      <td>928</td>\n",
       "      <td>694</td>\n",
       "      <td>...</td>\n",
       "      <td>1994</td>\n",
       "      <td>2891</td>\n",
       "      <td>483</td>\n",
       "      <td>525</td>\n",
       "      <td>889</td>\n",
       "      <td>1930</td>\n",
       "      <td>719</td>\n",
       "      <td>1839</td>\n",
       "      <td>746</td>\n",
       "      <td>AGRN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000078808</td>\n",
       "      <td>1230</td>\n",
       "      <td>1760</td>\n",
       "      <td>1567</td>\n",
       "      <td>1860</td>\n",
       "      <td>1262</td>\n",
       "      <td>1654</td>\n",
       "      <td>1035</td>\n",
       "      <td>1109</td>\n",
       "      <td>1488</td>\n",
       "      <td>...</td>\n",
       "      <td>5465</td>\n",
       "      <td>10102</td>\n",
       "      <td>3924</td>\n",
       "      <td>4388</td>\n",
       "      <td>3189</td>\n",
       "      <td>6184</td>\n",
       "      <td>4797</td>\n",
       "      <td>6962</td>\n",
       "      <td>6711</td>\n",
       "      <td>SDF4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000160087</td>\n",
       "      <td>796</td>\n",
       "      <td>896</td>\n",
       "      <td>680</td>\n",
       "      <td>786</td>\n",
       "      <td>748</td>\n",
       "      <td>839</td>\n",
       "      <td>443</td>\n",
       "      <td>576</td>\n",
       "      <td>732</td>\n",
       "      <td>...</td>\n",
       "      <td>1935</td>\n",
       "      <td>2553</td>\n",
       "      <td>1526</td>\n",
       "      <td>1579</td>\n",
       "      <td>1066</td>\n",
       "      <td>2029</td>\n",
       "      <td>1703</td>\n",
       "      <td>2905</td>\n",
       "      <td>2191</td>\n",
       "      <td>UBE2J2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9227</th>\n",
       "      <td>ENSG00000160294</td>\n",
       "      <td>3771</td>\n",
       "      <td>4043</td>\n",
       "      <td>3610</td>\n",
       "      <td>3821</td>\n",
       "      <td>3358</td>\n",
       "      <td>4222</td>\n",
       "      <td>2243</td>\n",
       "      <td>2785</td>\n",
       "      <td>3555</td>\n",
       "      <td>...</td>\n",
       "      <td>3556</td>\n",
       "      <td>5578</td>\n",
       "      <td>3769</td>\n",
       "      <td>5033</td>\n",
       "      <td>1902</td>\n",
       "      <td>4685</td>\n",
       "      <td>5744</td>\n",
       "      <td>6454</td>\n",
       "      <td>6584</td>\n",
       "      <td>MCM3AP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9228</th>\n",
       "      <td>ENSG00000182362</td>\n",
       "      <td>206</td>\n",
       "      <td>201</td>\n",
       "      <td>207</td>\n",
       "      <td>231</td>\n",
       "      <td>135</td>\n",
       "      <td>176</td>\n",
       "      <td>119</td>\n",
       "      <td>109</td>\n",
       "      <td>197</td>\n",
       "      <td>...</td>\n",
       "      <td>513</td>\n",
       "      <td>635</td>\n",
       "      <td>250</td>\n",
       "      <td>279</td>\n",
       "      <td>190</td>\n",
       "      <td>532</td>\n",
       "      <td>315</td>\n",
       "      <td>622</td>\n",
       "      <td>530</td>\n",
       "      <td>YBEY</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9229</th>\n",
       "      <td>ENSG00000160299</td>\n",
       "      <td>16989</td>\n",
       "      <td>13268</td>\n",
       "      <td>15518</td>\n",
       "      <td>15279</td>\n",
       "      <td>19910</td>\n",
       "      <td>18520</td>\n",
       "      <td>17353</td>\n",
       "      <td>16313</td>\n",
       "      <td>21883</td>\n",
       "      <td>...</td>\n",
       "      <td>11005</td>\n",
       "      <td>8842</td>\n",
       "      <td>15252</td>\n",
       "      <td>19719</td>\n",
       "      <td>3982</td>\n",
       "      <td>10027</td>\n",
       "      <td>32484</td>\n",
       "      <td>17641</td>\n",
       "      <td>39311</td>\n",
       "      <td>PCNT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9230</th>\n",
       "      <td>ENSG00000160305</td>\n",
       "      <td>3238</td>\n",
       "      <td>3501</td>\n",
       "      <td>2853</td>\n",
       "      <td>2824</td>\n",
       "      <td>2489</td>\n",
       "      <td>3200</td>\n",
       "      <td>1289</td>\n",
       "      <td>1808</td>\n",
       "      <td>2219</td>\n",
       "      <td>...</td>\n",
       "      <td>1329</td>\n",
       "      <td>2803</td>\n",
       "      <td>1851</td>\n",
       "      <td>2316</td>\n",
       "      <td>859</td>\n",
       "      <td>2701</td>\n",
       "      <td>2914</td>\n",
       "      <td>2095</td>\n",
       "      <td>3156</td>\n",
       "      <td>DIP2A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9231</th>\n",
       "      <td>ENSG00000160310</td>\n",
       "      <td>2144</td>\n",
       "      <td>2410</td>\n",
       "      <td>1532</td>\n",
       "      <td>1744</td>\n",
       "      <td>1151</td>\n",
       "      <td>1436</td>\n",
       "      <td>687</td>\n",
       "      <td>997</td>\n",
       "      <td>993</td>\n",
       "      <td>...</td>\n",
       "      <td>2779</td>\n",
       "      <td>8156</td>\n",
       "      <td>900</td>\n",
       "      <td>1091</td>\n",
       "      <td>1505</td>\n",
       "      <td>4738</td>\n",
       "      <td>1027</td>\n",
       "      <td>1761</td>\n",
       "      <td>913</td>\n",
       "      <td>PRMT2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9232 rows × 1223 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               GeneID  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  CDM-07  \\\n",
       "0     ENSG00000188976    1660    1657    1548    1598    1549    1785    1040   \n",
       "1     ENSG00000187642    2067    2606    5802    4378    5758    7291    4722   \n",
       "2     ENSG00000188157    1437    2687    1852    1500    1103    1049     570   \n",
       "3     ENSG00000078808    1230    1760    1567    1860    1262    1654    1035   \n",
       "4     ENSG00000160087     796     896     680     786     748     839     443   \n",
       "...               ...     ...     ...     ...     ...     ...     ...     ...   \n",
       "9227  ENSG00000160294    3771    4043    3610    3821    3358    4222    2243   \n",
       "9228  ENSG00000182362     206     201     207     231     135     176     119   \n",
       "9229  ENSG00000160299   16989   13268   15518   15279   19910   18520   17353   \n",
       "9230  ENSG00000160305    3238    3501    2853    2824    2489    3200    1289   \n",
       "9231  ENSG00000160310    2144    2410    1532    1744    1151    1436     687   \n",
       "\n",
       "      CDM-08  CDM-09  ...  9_FM3764  9_FM3796  9_FM3799  9_FM3800  9_FM3814  \\\n",
       "0       1221    1530  ...      3651      4258      3055      4565      1789   \n",
       "1       5029    7240  ...     12082      5923     14166     13120       597   \n",
       "2        928     694  ...      1994      2891       483       525       889   \n",
       "3       1109    1488  ...      5465     10102      3924      4388      3189   \n",
       "4        576     732  ...      1935      2553      1526      1579      1066   \n",
       "...      ...     ...  ...       ...       ...       ...       ...       ...   \n",
       "9227    2785    3555  ...      3556      5578      3769      5033      1902   \n",
       "9228     109     197  ...       513       635       250       279       190   \n",
       "9229   16313   21883  ...     11005      8842     15252     19719      3982   \n",
       "9230    1808    2219  ...      1329      2803      1851      2316       859   \n",
       "9231     997     993  ...      2779      8156       900      1091      1505   \n",
       "\n",
       "      9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  9_KO_AMP09  Symbol  \n",
       "0         4180           5231           8196        8402   NOC2L  \n",
       "1         4478           6682           4993        4021   PERM1  \n",
       "2         1930            719           1839         746    AGRN  \n",
       "3         6184           4797           6962        6711    SDF4  \n",
       "4         2029           1703           2905        2191  UBE2J2  \n",
       "...        ...            ...            ...         ...     ...  \n",
       "9227      4685           5744           6454        6584  MCM3AP  \n",
       "9228       532            315            622         530    YBEY  \n",
       "9229     10027          32484          17641       39311    PCNT  \n",
       "9230      2701           2914           2095        3156   DIP2A  \n",
       "9231      4738           1027           1761         913   PRMT2  \n",
       "\n",
       "[9232 rows x 1223 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "All_muscle['Symbol'] = All_muscle.GeneID.map(GeneID_dict)\n",
    "All_muscle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "All_muscle.drop_duplicates(subset='Symbol', keep=\"first\", inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GeneID</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "      <th>Symbol</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000188976</td>\n",
       "      <td>1660</td>\n",
       "      <td>1657</td>\n",
       "      <td>1548</td>\n",
       "      <td>1598</td>\n",
       "      <td>1549</td>\n",
       "      <td>1785</td>\n",
       "      <td>1040</td>\n",
       "      <td>1221</td>\n",
       "      <td>1530</td>\n",
       "      <td>...</td>\n",
       "      <td>3651</td>\n",
       "      <td>4258</td>\n",
       "      <td>3055</td>\n",
       "      <td>4565</td>\n",
       "      <td>1789</td>\n",
       "      <td>4180</td>\n",
       "      <td>5231</td>\n",
       "      <td>8196</td>\n",
       "      <td>8402</td>\n",
       "      <td>NOC2L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000187642</td>\n",
       "      <td>2067</td>\n",
       "      <td>2606</td>\n",
       "      <td>5802</td>\n",
       "      <td>4378</td>\n",
       "      <td>5758</td>\n",
       "      <td>7291</td>\n",
       "      <td>4722</td>\n",
       "      <td>5029</td>\n",
       "      <td>7240</td>\n",
       "      <td>...</td>\n",
       "      <td>12082</td>\n",
       "      <td>5923</td>\n",
       "      <td>14166</td>\n",
       "      <td>13120</td>\n",
       "      <td>597</td>\n",
       "      <td>4478</td>\n",
       "      <td>6682</td>\n",
       "      <td>4993</td>\n",
       "      <td>4021</td>\n",
       "      <td>PERM1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000188157</td>\n",
       "      <td>1437</td>\n",
       "      <td>2687</td>\n",
       "      <td>1852</td>\n",
       "      <td>1500</td>\n",
       "      <td>1103</td>\n",
       "      <td>1049</td>\n",
       "      <td>570</td>\n",
       "      <td>928</td>\n",
       "      <td>694</td>\n",
       "      <td>...</td>\n",
       "      <td>1994</td>\n",
       "      <td>2891</td>\n",
       "      <td>483</td>\n",
       "      <td>525</td>\n",
       "      <td>889</td>\n",
       "      <td>1930</td>\n",
       "      <td>719</td>\n",
       "      <td>1839</td>\n",
       "      <td>746</td>\n",
       "      <td>AGRN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000078808</td>\n",
       "      <td>1230</td>\n",
       "      <td>1760</td>\n",
       "      <td>1567</td>\n",
       "      <td>1860</td>\n",
       "      <td>1262</td>\n",
       "      <td>1654</td>\n",
       "      <td>1035</td>\n",
       "      <td>1109</td>\n",
       "      <td>1488</td>\n",
       "      <td>...</td>\n",
       "      <td>5465</td>\n",
       "      <td>10102</td>\n",
       "      <td>3924</td>\n",
       "      <td>4388</td>\n",
       "      <td>3189</td>\n",
       "      <td>6184</td>\n",
       "      <td>4797</td>\n",
       "      <td>6962</td>\n",
       "      <td>6711</td>\n",
       "      <td>SDF4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000160087</td>\n",
       "      <td>796</td>\n",
       "      <td>896</td>\n",
       "      <td>680</td>\n",
       "      <td>786</td>\n",
       "      <td>748</td>\n",
       "      <td>839</td>\n",
       "      <td>443</td>\n",
       "      <td>576</td>\n",
       "      <td>732</td>\n",
       "      <td>...</td>\n",
       "      <td>1935</td>\n",
       "      <td>2553</td>\n",
       "      <td>1526</td>\n",
       "      <td>1579</td>\n",
       "      <td>1066</td>\n",
       "      <td>2029</td>\n",
       "      <td>1703</td>\n",
       "      <td>2905</td>\n",
       "      <td>2191</td>\n",
       "      <td>UBE2J2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9227</th>\n",
       "      <td>ENSG00000160294</td>\n",
       "      <td>3771</td>\n",
       "      <td>4043</td>\n",
       "      <td>3610</td>\n",
       "      <td>3821</td>\n",
       "      <td>3358</td>\n",
       "      <td>4222</td>\n",
       "      <td>2243</td>\n",
       "      <td>2785</td>\n",
       "      <td>3555</td>\n",
       "      <td>...</td>\n",
       "      <td>3556</td>\n",
       "      <td>5578</td>\n",
       "      <td>3769</td>\n",
       "      <td>5033</td>\n",
       "      <td>1902</td>\n",
       "      <td>4685</td>\n",
       "      <td>5744</td>\n",
       "      <td>6454</td>\n",
       "      <td>6584</td>\n",
       "      <td>MCM3AP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9228</th>\n",
       "      <td>ENSG00000182362</td>\n",
       "      <td>206</td>\n",
       "      <td>201</td>\n",
       "      <td>207</td>\n",
       "      <td>231</td>\n",
       "      <td>135</td>\n",
       "      <td>176</td>\n",
       "      <td>119</td>\n",
       "      <td>109</td>\n",
       "      <td>197</td>\n",
       "      <td>...</td>\n",
       "      <td>513</td>\n",
       "      <td>635</td>\n",
       "      <td>250</td>\n",
       "      <td>279</td>\n",
       "      <td>190</td>\n",
       "      <td>532</td>\n",
       "      <td>315</td>\n",
       "      <td>622</td>\n",
       "      <td>530</td>\n",
       "      <td>YBEY</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9229</th>\n",
       "      <td>ENSG00000160299</td>\n",
       "      <td>16989</td>\n",
       "      <td>13268</td>\n",
       "      <td>15518</td>\n",
       "      <td>15279</td>\n",
       "      <td>19910</td>\n",
       "      <td>18520</td>\n",
       "      <td>17353</td>\n",
       "      <td>16313</td>\n",
       "      <td>21883</td>\n",
       "      <td>...</td>\n",
       "      <td>11005</td>\n",
       "      <td>8842</td>\n",
       "      <td>15252</td>\n",
       "      <td>19719</td>\n",
       "      <td>3982</td>\n",
       "      <td>10027</td>\n",
       "      <td>32484</td>\n",
       "      <td>17641</td>\n",
       "      <td>39311</td>\n",
       "      <td>PCNT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9230</th>\n",
       "      <td>ENSG00000160305</td>\n",
       "      <td>3238</td>\n",
       "      <td>3501</td>\n",
       "      <td>2853</td>\n",
       "      <td>2824</td>\n",
       "      <td>2489</td>\n",
       "      <td>3200</td>\n",
       "      <td>1289</td>\n",
       "      <td>1808</td>\n",
       "      <td>2219</td>\n",
       "      <td>...</td>\n",
       "      <td>1329</td>\n",
       "      <td>2803</td>\n",
       "      <td>1851</td>\n",
       "      <td>2316</td>\n",
       "      <td>859</td>\n",
       "      <td>2701</td>\n",
       "      <td>2914</td>\n",
       "      <td>2095</td>\n",
       "      <td>3156</td>\n",
       "      <td>DIP2A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9231</th>\n",
       "      <td>ENSG00000160310</td>\n",
       "      <td>2144</td>\n",
       "      <td>2410</td>\n",
       "      <td>1532</td>\n",
       "      <td>1744</td>\n",
       "      <td>1151</td>\n",
       "      <td>1436</td>\n",
       "      <td>687</td>\n",
       "      <td>997</td>\n",
       "      <td>993</td>\n",
       "      <td>...</td>\n",
       "      <td>2779</td>\n",
       "      <td>8156</td>\n",
       "      <td>900</td>\n",
       "      <td>1091</td>\n",
       "      <td>1505</td>\n",
       "      <td>4738</td>\n",
       "      <td>1027</td>\n",
       "      <td>1761</td>\n",
       "      <td>913</td>\n",
       "      <td>PRMT2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9231 rows × 1223 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               GeneID  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  CDM-07  \\\n",
       "0     ENSG00000188976    1660    1657    1548    1598    1549    1785    1040   \n",
       "1     ENSG00000187642    2067    2606    5802    4378    5758    7291    4722   \n",
       "2     ENSG00000188157    1437    2687    1852    1500    1103    1049     570   \n",
       "3     ENSG00000078808    1230    1760    1567    1860    1262    1654    1035   \n",
       "4     ENSG00000160087     796     896     680     786     748     839     443   \n",
       "...               ...     ...     ...     ...     ...     ...     ...     ...   \n",
       "9227  ENSG00000160294    3771    4043    3610    3821    3358    4222    2243   \n",
       "9228  ENSG00000182362     206     201     207     231     135     176     119   \n",
       "9229  ENSG00000160299   16989   13268   15518   15279   19910   18520   17353   \n",
       "9230  ENSG00000160305    3238    3501    2853    2824    2489    3200    1289   \n",
       "9231  ENSG00000160310    2144    2410    1532    1744    1151    1436     687   \n",
       "\n",
       "      CDM-08  CDM-09  ...  9_FM3764  9_FM3796  9_FM3799  9_FM3800  9_FM3814  \\\n",
       "0       1221    1530  ...      3651      4258      3055      4565      1789   \n",
       "1       5029    7240  ...     12082      5923     14166     13120       597   \n",
       "2        928     694  ...      1994      2891       483       525       889   \n",
       "3       1109    1488  ...      5465     10102      3924      4388      3189   \n",
       "4        576     732  ...      1935      2553      1526      1579      1066   \n",
       "...      ...     ...  ...       ...       ...       ...       ...       ...   \n",
       "9227    2785    3555  ...      3556      5578      3769      5033      1902   \n",
       "9228     109     197  ...       513       635       250       279       190   \n",
       "9229   16313   21883  ...     11005      8842     15252     19719      3982   \n",
       "9230    1808    2219  ...      1329      2803      1851      2316       859   \n",
       "9231     997     993  ...      2779      8156       900      1091      1505   \n",
       "\n",
       "      9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  9_KO_AMP09  Symbol  \n",
       "0         4180           5231           8196        8402   NOC2L  \n",
       "1         4478           6682           4993        4021   PERM1  \n",
       "2         1930            719           1839         746    AGRN  \n",
       "3         6184           4797           6962        6711    SDF4  \n",
       "4         2029           1703           2905        2191  UBE2J2  \n",
       "...        ...            ...            ...         ...     ...  \n",
       "9227      4685           5744           6454        6584  MCM3AP  \n",
       "9228       532            315            622         530    YBEY  \n",
       "9229     10027          32484          17641       39311    PCNT  \n",
       "9230      2701           2914           2095        3156   DIP2A  \n",
       "9231      4738           1027           1761         913   PRMT2  \n",
       "\n",
       "[9231 rows x 1223 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "All_muscle.to_csv('Integration data/All_muscle_L_raw.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Check if na cell exists in the integration table\n",
    "All_muscle.isna().sum().sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "9231"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(All_muscle['Symbol'].unique())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Symbol</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NOC2L</td>\n",
       "      <td>1660</td>\n",
       "      <td>1657</td>\n",
       "      <td>1548</td>\n",
       "      <td>1598</td>\n",
       "      <td>1549</td>\n",
       "      <td>1785</td>\n",
       "      <td>1040</td>\n",
       "      <td>1221</td>\n",
       "      <td>1530</td>\n",
       "      <td>...</td>\n",
       "      <td>3596</td>\n",
       "      <td>3651</td>\n",
       "      <td>4258</td>\n",
       "      <td>3055</td>\n",
       "      <td>4565</td>\n",
       "      <td>1789</td>\n",
       "      <td>4180</td>\n",
       "      <td>5231</td>\n",
       "      <td>8196</td>\n",
       "      <td>8402</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PERM1</td>\n",
       "      <td>2067</td>\n",
       "      <td>2606</td>\n",
       "      <td>5802</td>\n",
       "      <td>4378</td>\n",
       "      <td>5758</td>\n",
       "      <td>7291</td>\n",
       "      <td>4722</td>\n",
       "      <td>5029</td>\n",
       "      <td>7240</td>\n",
       "      <td>...</td>\n",
       "      <td>26682</td>\n",
       "      <td>12082</td>\n",
       "      <td>5923</td>\n",
       "      <td>14166</td>\n",
       "      <td>13120</td>\n",
       "      <td>597</td>\n",
       "      <td>4478</td>\n",
       "      <td>6682</td>\n",
       "      <td>4993</td>\n",
       "      <td>4021</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AGRN</td>\n",
       "      <td>1437</td>\n",
       "      <td>2687</td>\n",
       "      <td>1852</td>\n",
       "      <td>1500</td>\n",
       "      <td>1103</td>\n",
       "      <td>1049</td>\n",
       "      <td>570</td>\n",
       "      <td>928</td>\n",
       "      <td>694</td>\n",
       "      <td>...</td>\n",
       "      <td>555</td>\n",
       "      <td>1994</td>\n",
       "      <td>2891</td>\n",
       "      <td>483</td>\n",
       "      <td>525</td>\n",
       "      <td>889</td>\n",
       "      <td>1930</td>\n",
       "      <td>719</td>\n",
       "      <td>1839</td>\n",
       "      <td>746</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SDF4</td>\n",
       "      <td>1230</td>\n",
       "      <td>1760</td>\n",
       "      <td>1567</td>\n",
       "      <td>1860</td>\n",
       "      <td>1262</td>\n",
       "      <td>1654</td>\n",
       "      <td>1035</td>\n",
       "      <td>1109</td>\n",
       "      <td>1488</td>\n",
       "      <td>...</td>\n",
       "      <td>3418</td>\n",
       "      <td>5465</td>\n",
       "      <td>10102</td>\n",
       "      <td>3924</td>\n",
       "      <td>4388</td>\n",
       "      <td>3189</td>\n",
       "      <td>6184</td>\n",
       "      <td>4797</td>\n",
       "      <td>6962</td>\n",
       "      <td>6711</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBE2J2</td>\n",
       "      <td>796</td>\n",
       "      <td>896</td>\n",
       "      <td>680</td>\n",
       "      <td>786</td>\n",
       "      <td>748</td>\n",
       "      <td>839</td>\n",
       "      <td>443</td>\n",
       "      <td>576</td>\n",
       "      <td>732</td>\n",
       "      <td>...</td>\n",
       "      <td>1453</td>\n",
       "      <td>1935</td>\n",
       "      <td>2553</td>\n",
       "      <td>1526</td>\n",
       "      <td>1579</td>\n",
       "      <td>1066</td>\n",
       "      <td>2029</td>\n",
       "      <td>1703</td>\n",
       "      <td>2905</td>\n",
       "      <td>2191</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9227</th>\n",
       "      <td>MCM3AP</td>\n",
       "      <td>3771</td>\n",
       "      <td>4043</td>\n",
       "      <td>3610</td>\n",
       "      <td>3821</td>\n",
       "      <td>3358</td>\n",
       "      <td>4222</td>\n",
       "      <td>2243</td>\n",
       "      <td>2785</td>\n",
       "      <td>3555</td>\n",
       "      <td>...</td>\n",
       "      <td>4292</td>\n",
       "      <td>3556</td>\n",
       "      <td>5578</td>\n",
       "      <td>3769</td>\n",
       "      <td>5033</td>\n",
       "      <td>1902</td>\n",
       "      <td>4685</td>\n",
       "      <td>5744</td>\n",
       "      <td>6454</td>\n",
       "      <td>6584</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9228</th>\n",
       "      <td>YBEY</td>\n",
       "      <td>206</td>\n",
       "      <td>201</td>\n",
       "      <td>207</td>\n",
       "      <td>231</td>\n",
       "      <td>135</td>\n",
       "      <td>176</td>\n",
       "      <td>119</td>\n",
       "      <td>109</td>\n",
       "      <td>197</td>\n",
       "      <td>...</td>\n",
       "      <td>351</td>\n",
       "      <td>513</td>\n",
       "      <td>635</td>\n",
       "      <td>250</td>\n",
       "      <td>279</td>\n",
       "      <td>190</td>\n",
       "      <td>532</td>\n",
       "      <td>315</td>\n",
       "      <td>622</td>\n",
       "      <td>530</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9229</th>\n",
       "      <td>PCNT</td>\n",
       "      <td>16989</td>\n",
       "      <td>13268</td>\n",
       "      <td>15518</td>\n",
       "      <td>15279</td>\n",
       "      <td>19910</td>\n",
       "      <td>18520</td>\n",
       "      <td>17353</td>\n",
       "      <td>16313</td>\n",
       "      <td>21883</td>\n",
       "      <td>...</td>\n",
       "      <td>18572</td>\n",
       "      <td>11005</td>\n",
       "      <td>8842</td>\n",
       "      <td>15252</td>\n",
       "      <td>19719</td>\n",
       "      <td>3982</td>\n",
       "      <td>10027</td>\n",
       "      <td>32484</td>\n",
       "      <td>17641</td>\n",
       "      <td>39311</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9230</th>\n",
       "      <td>DIP2A</td>\n",
       "      <td>3238</td>\n",
       "      <td>3501</td>\n",
       "      <td>2853</td>\n",
       "      <td>2824</td>\n",
       "      <td>2489</td>\n",
       "      <td>3200</td>\n",
       "      <td>1289</td>\n",
       "      <td>1808</td>\n",
       "      <td>2219</td>\n",
       "      <td>...</td>\n",
       "      <td>1288</td>\n",
       "      <td>1329</td>\n",
       "      <td>2803</td>\n",
       "      <td>1851</td>\n",
       "      <td>2316</td>\n",
       "      <td>859</td>\n",
       "      <td>2701</td>\n",
       "      <td>2914</td>\n",
       "      <td>2095</td>\n",
       "      <td>3156</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9231</th>\n",
       "      <td>PRMT2</td>\n",
       "      <td>2144</td>\n",
       "      <td>2410</td>\n",
       "      <td>1532</td>\n",
       "      <td>1744</td>\n",
       "      <td>1151</td>\n",
       "      <td>1436</td>\n",
       "      <td>687</td>\n",
       "      <td>997</td>\n",
       "      <td>993</td>\n",
       "      <td>...</td>\n",
       "      <td>1087</td>\n",
       "      <td>2779</td>\n",
       "      <td>8156</td>\n",
       "      <td>900</td>\n",
       "      <td>1091</td>\n",
       "      <td>1505</td>\n",
       "      <td>4738</td>\n",
       "      <td>1027</td>\n",
       "      <td>1761</td>\n",
       "      <td>913</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9231 rows × 1222 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Symbol  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  CDM-07  CDM-08  \\\n",
       "0      NOC2L    1660    1657    1548    1598    1549    1785    1040    1221   \n",
       "1      PERM1    2067    2606    5802    4378    5758    7291    4722    5029   \n",
       "2       AGRN    1437    2687    1852    1500    1103    1049     570     928   \n",
       "3       SDF4    1230    1760    1567    1860    1262    1654    1035    1109   \n",
       "4     UBE2J2     796     896     680     786     748     839     443     576   \n",
       "...      ...     ...     ...     ...     ...     ...     ...     ...     ...   \n",
       "9227  MCM3AP    3771    4043    3610    3821    3358    4222    2243    2785   \n",
       "9228    YBEY     206     201     207     231     135     176     119     109   \n",
       "9229    PCNT   16989   13268   15518   15279   19910   18520   17353   16313   \n",
       "9230   DIP2A    3238    3501    2853    2824    2489    3200    1289    1808   \n",
       "9231   PRMT2    2144    2410    1532    1744    1151    1436     687     997   \n",
       "\n",
       "      CDM-09  ...  9_FM3690_2  9_FM3764  9_FM3796  9_FM3799  9_FM3800  \\\n",
       "0       1530  ...        3596      3651      4258      3055      4565   \n",
       "1       7240  ...       26682     12082      5923     14166     13120   \n",
       "2        694  ...         555      1994      2891       483       525   \n",
       "3       1488  ...        3418      5465     10102      3924      4388   \n",
       "4        732  ...        1453      1935      2553      1526      1579   \n",
       "...      ...  ...         ...       ...       ...       ...       ...   \n",
       "9227    3555  ...        4292      3556      5578      3769      5033   \n",
       "9228     197  ...         351       513       635       250       279   \n",
       "9229   21883  ...       18572     11005      8842     15252     19719   \n",
       "9230    2219  ...        1288      1329      2803      1851      2316   \n",
       "9231     993  ...        1087      2779      8156       900      1091   \n",
       "\n",
       "      9_FM3814  9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  9_KO_AMP09  \n",
       "0         1789      4180           5231           8196        8402  \n",
       "1          597      4478           6682           4993        4021  \n",
       "2          889      1930            719           1839         746  \n",
       "3         3189      6184           4797           6962        6711  \n",
       "4         1066      2029           1703           2905        2191  \n",
       "...        ...       ...            ...            ...         ...  \n",
       "9227      1902      4685           5744           6454        6584  \n",
       "9228       190       532            315            622         530  \n",
       "9229      3982     10027          32484          17641       39311  \n",
       "9230       859      2701           2914           2095        3156  \n",
       "9231      1505      4738           1027           1761         913  \n",
       "\n",
       "[9231 rows x 1222 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "All_muscle = pd.concat([ All_muscle['Symbol'], All_muscle.loc[:, 'CDM-01':'9_KO_AMP09'] ], axis=1)\n",
    "All_muscle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "All_muscle.to_csv('Integration data/All_muscle_L_raw.csv', index=False)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#  Batch effect adjustification (ComBat-seq) - R\n",
    "- Please prosess this step in **R1 Batch effect adjustment combat-seq.R**"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Normalization (TMM)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Symbol</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NOC2L</td>\n",
       "      <td>3399</td>\n",
       "      <td>3387</td>\n",
       "      <td>3039</td>\n",
       "      <td>3078</td>\n",
       "      <td>3084</td>\n",
       "      <td>3548</td>\n",
       "      <td>1893</td>\n",
       "      <td>2257</td>\n",
       "      <td>2837</td>\n",
       "      <td>...</td>\n",
       "      <td>2740</td>\n",
       "      <td>2717</td>\n",
       "      <td>3140</td>\n",
       "      <td>2340</td>\n",
       "      <td>3244</td>\n",
       "      <td>1250</td>\n",
       "      <td>2980</td>\n",
       "      <td>3627</td>\n",
       "      <td>5367</td>\n",
       "      <td>5385</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PERM1</td>\n",
       "      <td>1620</td>\n",
       "      <td>2612</td>\n",
       "      <td>10648</td>\n",
       "      <td>5934</td>\n",
       "      <td>10916</td>\n",
       "      <td>14637</td>\n",
       "      <td>8130</td>\n",
       "      <td>8390</td>\n",
       "      <td>13469</td>\n",
       "      <td>...</td>\n",
       "      <td>23745</td>\n",
       "      <td>11063</td>\n",
       "      <td>5661</td>\n",
       "      <td>12859</td>\n",
       "      <td>11955</td>\n",
       "      <td>614</td>\n",
       "      <td>4300</td>\n",
       "      <td>6296</td>\n",
       "      <td>4812</td>\n",
       "      <td>3899</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AGRN</td>\n",
       "      <td>1201</td>\n",
       "      <td>2553</td>\n",
       "      <td>1604</td>\n",
       "      <td>1202</td>\n",
       "      <td>849</td>\n",
       "      <td>760</td>\n",
       "      <td>360</td>\n",
       "      <td>669</td>\n",
       "      <td>418</td>\n",
       "      <td>...</td>\n",
       "      <td>277</td>\n",
       "      <td>830</td>\n",
       "      <td>1171</td>\n",
       "      <td>241</td>\n",
       "      <td>259</td>\n",
       "      <td>361</td>\n",
       "      <td>798</td>\n",
       "      <td>339</td>\n",
       "      <td>779</td>\n",
       "      <td>349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SDF4</td>\n",
       "      <td>2743</td>\n",
       "      <td>4648</td>\n",
       "      <td>3754</td>\n",
       "      <td>4601</td>\n",
       "      <td>2783</td>\n",
       "      <td>3885</td>\n",
       "      <td>2116</td>\n",
       "      <td>2220</td>\n",
       "      <td>3120</td>\n",
       "      <td>...</td>\n",
       "      <td>1849</td>\n",
       "      <td>2843</td>\n",
       "      <td>5102</td>\n",
       "      <td>2081</td>\n",
       "      <td>2311</td>\n",
       "      <td>1611</td>\n",
       "      <td>3174</td>\n",
       "      <td>2512</td>\n",
       "      <td>3585</td>\n",
       "      <td>3440</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBE2J2</td>\n",
       "      <td>1667</td>\n",
       "      <td>1926</td>\n",
       "      <td>1332</td>\n",
       "      <td>1557</td>\n",
       "      <td>1524</td>\n",
       "      <td>1696</td>\n",
       "      <td>793</td>\n",
       "      <td>1081</td>\n",
       "      <td>1384</td>\n",
       "      <td>...</td>\n",
       "      <td>1050</td>\n",
       "      <td>1355</td>\n",
       "      <td>1764</td>\n",
       "      <td>1086</td>\n",
       "      <td>1121</td>\n",
       "      <td>723</td>\n",
       "      <td>1405</td>\n",
       "      <td>1202</td>\n",
       "      <td>1984</td>\n",
       "      <td>1515</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9226</th>\n",
       "      <td>MCM3AP</td>\n",
       "      <td>4491</td>\n",
       "      <td>4894</td>\n",
       "      <td>4135</td>\n",
       "      <td>4317</td>\n",
       "      <td>3828</td>\n",
       "      <td>4919</td>\n",
       "      <td>2307</td>\n",
       "      <td>2967</td>\n",
       "      <td>3823</td>\n",
       "      <td>...</td>\n",
       "      <td>3486</td>\n",
       "      <td>2835</td>\n",
       "      <td>4786</td>\n",
       "      <td>3067</td>\n",
       "      <td>4341</td>\n",
       "      <td>1660</td>\n",
       "      <td>4040</td>\n",
       "      <td>5084</td>\n",
       "      <td>5727</td>\n",
       "      <td>5986</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9227</th>\n",
       "      <td>YBEY</td>\n",
       "      <td>298</td>\n",
       "      <td>288</td>\n",
       "      <td>290</td>\n",
       "      <td>325</td>\n",
       "      <td>166</td>\n",
       "      <td>226</td>\n",
       "      <td>143</td>\n",
       "      <td>121</td>\n",
       "      <td>254</td>\n",
       "      <td>...</td>\n",
       "      <td>174</td>\n",
       "      <td>260</td>\n",
       "      <td>322</td>\n",
       "      <td>123</td>\n",
       "      <td>138</td>\n",
       "      <td>97</td>\n",
       "      <td>271</td>\n",
       "      <td>156</td>\n",
       "      <td>316</td>\n",
       "      <td>269</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9228</th>\n",
       "      <td>PCNT</td>\n",
       "      <td>26829</td>\n",
       "      <td>17973</td>\n",
       "      <td>21846</td>\n",
       "      <td>19885</td>\n",
       "      <td>33411</td>\n",
       "      <td>27427</td>\n",
       "      <td>27951</td>\n",
       "      <td>23852</td>\n",
       "      <td>33561</td>\n",
       "      <td>...</td>\n",
       "      <td>29710</td>\n",
       "      <td>18628</td>\n",
       "      <td>15700</td>\n",
       "      <td>24587</td>\n",
       "      <td>30816</td>\n",
       "      <td>6702</td>\n",
       "      <td>16969</td>\n",
       "      <td>47996</td>\n",
       "      <td>28303</td>\n",
       "      <td>56932</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9229</th>\n",
       "      <td>DIP2A</td>\n",
       "      <td>2532</td>\n",
       "      <td>2754</td>\n",
       "      <td>2186</td>\n",
       "      <td>2140</td>\n",
       "      <td>1892</td>\n",
       "      <td>2456</td>\n",
       "      <td>918</td>\n",
       "      <td>1324</td>\n",
       "      <td>1623</td>\n",
       "      <td>...</td>\n",
       "      <td>806</td>\n",
       "      <td>886</td>\n",
       "      <td>2409</td>\n",
       "      <td>1438</td>\n",
       "      <td>1948</td>\n",
       "      <td>733</td>\n",
       "      <td>2449</td>\n",
       "      <td>2649</td>\n",
       "      <td>1637</td>\n",
       "      <td>2952</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9230</th>\n",
       "      <td>PRMT2</td>\n",
       "      <td>2663</td>\n",
       "      <td>3075</td>\n",
       "      <td>1681</td>\n",
       "      <td>1928</td>\n",
       "      <td>1169</td>\n",
       "      <td>1495</td>\n",
       "      <td>583</td>\n",
       "      <td>944</td>\n",
       "      <td>860</td>\n",
       "      <td>...</td>\n",
       "      <td>639</td>\n",
       "      <td>1264</td>\n",
       "      <td>3086</td>\n",
       "      <td>536</td>\n",
       "      <td>619</td>\n",
       "      <td>626</td>\n",
       "      <td>1902</td>\n",
       "      <td>591</td>\n",
       "      <td>906</td>\n",
       "      <td>541</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9231 rows × 1222 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Symbol  CDM-01  CDM-02  CDM-03  CDM-04  CDM-05  CDM-06  CDM-07  CDM-08  \\\n",
       "0      NOC2L    3399    3387    3039    3078    3084    3548    1893    2257   \n",
       "1      PERM1    1620    2612   10648    5934   10916   14637    8130    8390   \n",
       "2       AGRN    1201    2553    1604    1202     849     760     360     669   \n",
       "3       SDF4    2743    4648    3754    4601    2783    3885    2116    2220   \n",
       "4     UBE2J2    1667    1926    1332    1557    1524    1696     793    1081   \n",
       "...      ...     ...     ...     ...     ...     ...     ...     ...     ...   \n",
       "9226  MCM3AP    4491    4894    4135    4317    3828    4919    2307    2967   \n",
       "9227    YBEY     298     288     290     325     166     226     143     121   \n",
       "9228    PCNT   26829   17973   21846   19885   33411   27427   27951   23852   \n",
       "9229   DIP2A    2532    2754    2186    2140    1892    2456     918    1324   \n",
       "9230   PRMT2    2663    3075    1681    1928    1169    1495     583     944   \n",
       "\n",
       "      CDM-09  ...  9_FM3690_2  9_FM3764  9_FM3796  9_FM3799  9_FM3800  \\\n",
       "0       2837  ...        2740      2717      3140      2340      3244   \n",
       "1      13469  ...       23745     11063      5661     12859     11955   \n",
       "2        418  ...         277       830      1171       241       259   \n",
       "3       3120  ...        1849      2843      5102      2081      2311   \n",
       "4       1384  ...        1050      1355      1764      1086      1121   \n",
       "...      ...  ...         ...       ...       ...       ...       ...   \n",
       "9226    3823  ...        3486      2835      4786      3067      4341   \n",
       "9227     254  ...         174       260       322       123       138   \n",
       "9228   33561  ...       29710     18628     15700     24587     30816   \n",
       "9229    1623  ...         806       886      2409      1438      1948   \n",
       "9230     860  ...         639      1264      3086       536       619   \n",
       "\n",
       "      9_FM3814  9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  9_KO_AMP09  \n",
       "0         1250      2980           3627           5367        5385  \n",
       "1          614      4300           6296           4812        3899  \n",
       "2          361       798            339            779         349  \n",
       "3         1611      3174           2512           3585        3440  \n",
       "4          723      1405           1202           1984        1515  \n",
       "...        ...       ...            ...            ...         ...  \n",
       "9226      1660      4040           5084           5727        5986  \n",
       "9227        97       271            156            316         269  \n",
       "9228      6702     16969          47996          28303       56932  \n",
       "9229       733      2449           2649           1637        2952  \n",
       "9230       626      1902            591            906         541  \n",
       "\n",
       "[9231 rows x 1222 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merge_L_combat = pd.read_csv('Integration data/All_muscle_L_combatseq.csv', delimiter='\t')\n",
    "merge_L_combat.dropna(inplace = True)\n",
    "merge_L_combat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Symbol</th>\n",
       "      <th>CDM-01</th>\n",
       "      <th>CDM-02</th>\n",
       "      <th>CDM-03</th>\n",
       "      <th>CDM-04</th>\n",
       "      <th>CDM-05</th>\n",
       "      <th>CDM-06</th>\n",
       "      <th>CDM-07</th>\n",
       "      <th>CDM-08</th>\n",
       "      <th>CDM-09</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NOC2L</td>\n",
       "      <td>2131.013236</td>\n",
       "      <td>2026.624297</td>\n",
       "      <td>2161.732859</td>\n",
       "      <td>2239.702980</td>\n",
       "      <td>2259.277316</td>\n",
       "      <td>2657.465623</td>\n",
       "      <td>2029.105981</td>\n",
       "      <td>2062.450073</td>\n",
       "      <td>2768.389544</td>\n",
       "      <td>...</td>\n",
       "      <td>3915.296361</td>\n",
       "      <td>2973.716215</td>\n",
       "      <td>1960.376048</td>\n",
       "      <td>2898.501889</td>\n",
       "      <td>3811.774838</td>\n",
       "      <td>1028.062029</td>\n",
       "      <td>2409.192285</td>\n",
       "      <td>3899.836861</td>\n",
       "      <td>5000.246936</td>\n",
       "      <td>5165.570071</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PERM1</td>\n",
       "      <td>1015.663855</td>\n",
       "      <td>1562.900107</td>\n",
       "      <td>7574.245304</td>\n",
       "      <td>4317.867929</td>\n",
       "      <td>7996.845388</td>\n",
       "      <td>10963.169201</td>\n",
       "      <td>8714.543912</td>\n",
       "      <td>7666.794911</td>\n",
       "      <td>13143.263577</td>\n",
       "      <td>...</td>\n",
       "      <td>33930.186896</td>\n",
       "      <td>12108.289467</td>\n",
       "      <td>3534.295798</td>\n",
       "      <td>15928.134953</td>\n",
       "      <td>14047.400799</td>\n",
       "      <td>504.984069</td>\n",
       "      <td>3476.351284</td>\n",
       "      <td>6769.609285</td>\n",
       "      <td>4483.172769</td>\n",
       "      <td>3740.122137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AGRN</td>\n",
       "      <td>752.970549</td>\n",
       "      <td>1527.597234</td>\n",
       "      <td>1140.973842</td>\n",
       "      <td>874.633847</td>\n",
       "      <td>621.960584</td>\n",
       "      <td>569.242918</td>\n",
       "      <td>385.883863</td>\n",
       "      <td>611.333229</td>\n",
       "      <td>407.891022</td>\n",
       "      <td>...</td>\n",
       "      <td>395.816457</td>\n",
       "      <td>908.422693</td>\n",
       "      <td>731.082915</td>\n",
       "      <td>298.520921</td>\n",
       "      <td>304.330975</td>\n",
       "      <td>296.904314</td>\n",
       "      <td>645.146122</td>\n",
       "      <td>364.500881</td>\n",
       "      <td>725.767163</td>\n",
       "      <td>334.778822</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SDF4</td>\n",
       "      <td>1719.732070</td>\n",
       "      <td>2781.148430</td>\n",
       "      <td>2670.334041</td>\n",
       "      <td>3347.912090</td>\n",
       "      <td>2038.770678</td>\n",
       "      <td>2909.879917</td>\n",
       "      <td>2268.139596</td>\n",
       "      <td>2028.639416</td>\n",
       "      <td>3044.545427</td>\n",
       "      <td>...</td>\n",
       "      <td>2642.110574</td>\n",
       "      <td>3111.621346</td>\n",
       "      <td>3185.298916</td>\n",
       "      <td>2577.684800</td>\n",
       "      <td>2715.478314</td>\n",
       "      <td>1324.966343</td>\n",
       "      <td>2566.032320</td>\n",
       "      <td>2700.962282</td>\n",
       "      <td>3340.019613</td>\n",
       "      <td>3299.825635</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBE2J2</td>\n",
       "      <td>1045.130646</td>\n",
       "      <td>1152.429405</td>\n",
       "      <td>947.491993</td>\n",
       "      <td>1132.949168</td>\n",
       "      <td>1116.452214</td>\n",
       "      <td>1270.310512</td>\n",
       "      <td>850.016399</td>\n",
       "      <td>987.819463</td>\n",
       "      <td>1350.529125</td>\n",
       "      <td>...</td>\n",
       "      <td>1500.387292</td>\n",
       "      <td>1483.027409</td>\n",
       "      <td>1101.306799</td>\n",
       "      <td>1345.202159</td>\n",
       "      <td>1317.200861</td>\n",
       "      <td>594.631077</td>\n",
       "      <td>1135.877571</td>\n",
       "      <td>1292.419054</td>\n",
       "      <td>1848.423685</td>\n",
       "      <td>1453.266232</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9226</th>\n",
       "      <td>MCM3AP</td>\n",
       "      <td>2815.645909</td>\n",
       "      <td>2928.343463</td>\n",
       "      <td>2941.350895</td>\n",
       "      <td>3141.259833</td>\n",
       "      <td>2804.316979</td>\n",
       "      <td>3684.349887</td>\n",
       "      <td>2472.872424</td>\n",
       "      <td>2711.249166</td>\n",
       "      <td>3730.543964</td>\n",
       "      <td>...</td>\n",
       "      <td>4981.285808</td>\n",
       "      <td>3102.865465</td>\n",
       "      <td>2988.012664</td>\n",
       "      <td>3799.019356</td>\n",
       "      <td>5100.775146</td>\n",
       "      <td>1365.266374</td>\n",
       "      <td>3266.153299</td>\n",
       "      <td>5466.437993</td>\n",
       "      <td>5335.646395</td>\n",
       "      <td>5742.080306</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9227</th>\n",
       "      <td>YBEY</td>\n",
       "      <td>186.831993</td>\n",
       "      <td>172.325892</td>\n",
       "      <td>206.285794</td>\n",
       "      <td>236.485857</td>\n",
       "      <td>121.608312</td>\n",
       "      <td>169.274868</td>\n",
       "      <td>153.281646</td>\n",
       "      <td>110.569986</td>\n",
       "      <td>247.857224</td>\n",
       "      <td>...</td>\n",
       "      <td>248.635608</td>\n",
       "      <td>284.566145</td>\n",
       "      <td>201.032193</td>\n",
       "      <td>152.357151</td>\n",
       "      <td>162.153184</td>\n",
       "      <td>79.777613</td>\n",
       "      <td>219.090976</td>\n",
       "      <td>167.734919</td>\n",
       "      <td>294.406192</td>\n",
       "      <td>258.038691</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9228</th>\n",
       "      <td>PCNT</td>\n",
       "      <td>16820.521951</td>\n",
       "      <td>10754.212722</td>\n",
       "      <td>15539.722287</td>\n",
       "      <td>14469.296219</td>\n",
       "      <td>24476.236833</td>\n",
       "      <td>20542.928311</td>\n",
       "      <td>29960.666283</td>\n",
       "      <td>21795.994304</td>\n",
       "      <td>32749.355477</td>\n",
       "      <td>...</td>\n",
       "      <td>42453.815653</td>\n",
       "      <td>20388.069799</td>\n",
       "      <td>9801.880238</td>\n",
       "      <td>30455.327326</td>\n",
       "      <td>36209.510917</td>\n",
       "      <td>5512.057374</td>\n",
       "      <td>13718.652309</td>\n",
       "      <td>51606.443339</td>\n",
       "      <td>26368.919138</td>\n",
       "      <td>54612.114262</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9229</th>\n",
       "      <td>DIP2A</td>\n",
       "      <td>1587.444988</td>\n",
       "      <td>1647.866346</td>\n",
       "      <td>1554.968091</td>\n",
       "      <td>1557.168414</td>\n",
       "      <td>1386.041725</td>\n",
       "      <td>1839.553430</td>\n",
       "      <td>984.003851</td>\n",
       "      <td>1209.873237</td>\n",
       "      <td>1583.749112</td>\n",
       "      <td>...</td>\n",
       "      <td>1151.725864</td>\n",
       "      <td>969.713863</td>\n",
       "      <td>1503.995509</td>\n",
       "      <td>1781.216118</td>\n",
       "      <td>2288.944940</td>\n",
       "      <td>602.855574</td>\n",
       "      <td>1979.903324</td>\n",
       "      <td>2848.267947</td>\n",
       "      <td>1525.135874</td>\n",
       "      <td>2831.710836</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9230</th>\n",
       "      <td>PRMT2</td>\n",
       "      <td>1669.575830</td>\n",
       "      <td>1839.937914</td>\n",
       "      <td>1195.746277</td>\n",
       "      <td>1402.906870</td>\n",
       "      <td>856.386246</td>\n",
       "      <td>1119.760740</td>\n",
       "      <td>624.917479</td>\n",
       "      <td>862.628653</td>\n",
       "      <td>839.201624</td>\n",
       "      <td>...</td>\n",
       "      <td>913.092837</td>\n",
       "      <td>1383.429258</td>\n",
       "      <td>1926.662574</td>\n",
       "      <td>663.930347</td>\n",
       "      <td>727.339280</td>\n",
       "      <td>514.853464</td>\n",
       "      <td>1537.679103</td>\n",
       "      <td>635.457288</td>\n",
       "      <td>844.088639</td>\n",
       "      <td>518.955136</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9231 rows × 1222 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Symbol        CDM-01        CDM-02        CDM-03        CDM-04  \\\n",
       "0      NOC2L   2131.013236   2026.624297   2161.732859   2239.702980   \n",
       "1      PERM1   1015.663855   1562.900107   7574.245304   4317.867929   \n",
       "2       AGRN    752.970549   1527.597234   1140.973842    874.633847   \n",
       "3       SDF4   1719.732070   2781.148430   2670.334041   3347.912090   \n",
       "4     UBE2J2   1045.130646   1152.429405    947.491993   1132.949168   \n",
       "...      ...           ...           ...           ...           ...   \n",
       "9226  MCM3AP   2815.645909   2928.343463   2941.350895   3141.259833   \n",
       "9227    YBEY    186.831993    172.325892    206.285794    236.485857   \n",
       "9228    PCNT  16820.521951  10754.212722  15539.722287  14469.296219   \n",
       "9229   DIP2A   1587.444988   1647.866346   1554.968091   1557.168414   \n",
       "9230   PRMT2   1669.575830   1839.937914   1195.746277   1402.906870   \n",
       "\n",
       "            CDM-05        CDM-06        CDM-07        CDM-08        CDM-09  \\\n",
       "0      2259.277316   2657.465623   2029.105981   2062.450073   2768.389544   \n",
       "1      7996.845388  10963.169201   8714.543912   7666.794911  13143.263577   \n",
       "2       621.960584    569.242918    385.883863    611.333229    407.891022   \n",
       "3      2038.770678   2909.879917   2268.139596   2028.639416   3044.545427   \n",
       "4      1116.452214   1270.310512    850.016399    987.819463   1350.529125   \n",
       "...            ...           ...           ...           ...           ...   \n",
       "9226   2804.316979   3684.349887   2472.872424   2711.249166   3730.543964   \n",
       "9227    121.608312    169.274868    153.281646    110.569986    247.857224   \n",
       "9228  24476.236833  20542.928311  29960.666283  21795.994304  32749.355477   \n",
       "9229   1386.041725   1839.553430    984.003851   1209.873237   1583.749112   \n",
       "9230    856.386246   1119.760740    624.917479    862.628653    839.201624   \n",
       "\n",
       "      ...    9_FM3690_2      9_FM3764     9_FM3796      9_FM3799  \\\n",
       "0     ...   3915.296361   2973.716215  1960.376048   2898.501889   \n",
       "1     ...  33930.186896  12108.289467  3534.295798  15928.134953   \n",
       "2     ...    395.816457    908.422693   731.082915    298.520921   \n",
       "3     ...   2642.110574   3111.621346  3185.298916   2577.684800   \n",
       "4     ...   1500.387292   1483.027409  1101.306799   1345.202159   \n",
       "...   ...           ...           ...          ...           ...   \n",
       "9226  ...   4981.285808   3102.865465  2988.012664   3799.019356   \n",
       "9227  ...    248.635608    284.566145   201.032193    152.357151   \n",
       "9228  ...  42453.815653  20388.069799  9801.880238  30455.327326   \n",
       "9229  ...   1151.725864    969.713863  1503.995509   1781.216118   \n",
       "9230  ...    913.092837   1383.429258  1926.662574    663.930347   \n",
       "\n",
       "          9_FM3800     9_FM3814      9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  \\\n",
       "0      3811.774838  1028.062029   2409.192285    3899.836861    5000.246936   \n",
       "1     14047.400799   504.984069   3476.351284    6769.609285    4483.172769   \n",
       "2       304.330975   296.904314    645.146122     364.500881     725.767163   \n",
       "3      2715.478314  1324.966343   2566.032320    2700.962282    3340.019613   \n",
       "4      1317.200861   594.631077   1135.877571    1292.419054    1848.423685   \n",
       "...            ...          ...           ...            ...            ...   \n",
       "9226   5100.775146  1365.266374   3266.153299    5466.437993    5335.646395   \n",
       "9227    162.153184    79.777613    219.090976     167.734919     294.406192   \n",
       "9228  36209.510917  5512.057374  13718.652309   51606.443339   26368.919138   \n",
       "9229   2288.944940   602.855574   1979.903324    2848.267947    1525.135874   \n",
       "9230    727.339280   514.853464   1537.679103     635.457288     844.088639   \n",
       "\n",
       "        9_KO_AMP09  \n",
       "0      5165.570071  \n",
       "1      3740.122137  \n",
       "2       334.778822  \n",
       "3      3299.825635  \n",
       "4      1453.266232  \n",
       "...            ...  \n",
       "9226   5742.080306  \n",
       "9227    258.038691  \n",
       "9228  54612.114262  \n",
       "9229   2831.710836  \n",
       "9230    518.955136  \n",
       "\n",
       "[9231 rows x 1222 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import conorm\n",
    "\n",
    "merge_L_tmm = conorm.tmm(merge_L_combat.iloc[:, 1:])\n",
    "merge_L_combat.iloc[:, 1:] = merge_L_tmm\n",
    "merge_L_combat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "merge_L_combat.to_csv('Integration data/All_muscle_L_combatseq_tmm.csv', index=False)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Transpose (for scanpy reading)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "merge_L_combat_tmm =  pd.read_csv('Integration data/All_muscle_L_combatseq_tmm.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>Symbol</th>\n",
       "      <th>NOC2L</th>\n",
       "      <th>PERM1</th>\n",
       "      <th>AGRN</th>\n",
       "      <th>SDF4</th>\n",
       "      <th>UBE2J2</th>\n",
       "      <th>ACAP3</th>\n",
       "      <th>INTS11</th>\n",
       "      <th>CPTP</th>\n",
       "      <th>DVL1</th>\n",
       "      <th>MXRA8</th>\n",
       "      <th>...</th>\n",
       "      <th>POFUT2</th>\n",
       "      <th>COL18A1</th>\n",
       "      <th>COL6A1</th>\n",
       "      <th>COL6A2</th>\n",
       "      <th>LSS</th>\n",
       "      <th>MCM3AP</th>\n",
       "      <th>YBEY</th>\n",
       "      <th>PCNT</th>\n",
       "      <th>DIP2A</th>\n",
       "      <th>PRMT2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>CDM-01</th>\n",
       "      <td>2131.013236</td>\n",
       "      <td>1015.663855</td>\n",
       "      <td>752.970549</td>\n",
       "      <td>1719.732070</td>\n",
       "      <td>1045.130646</td>\n",
       "      <td>1909.698828</td>\n",
       "      <td>2885.864644</td>\n",
       "      <td>505.324115</td>\n",
       "      <td>3567.989505</td>\n",
       "      <td>3157.335292</td>\n",
       "      <td>...</td>\n",
       "      <td>660.808459</td>\n",
       "      <td>2386.810059</td>\n",
       "      <td>4548.543992</td>\n",
       "      <td>5520.321137</td>\n",
       "      <td>1261.429430</td>\n",
       "      <td>2815.645909</td>\n",
       "      <td>186.831993</td>\n",
       "      <td>16820.521951</td>\n",
       "      <td>1587.444988</td>\n",
       "      <td>1669.575830</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CDM-02</th>\n",
       "      <td>2026.624297</td>\n",
       "      <td>1562.900107</td>\n",
       "      <td>1527.597234</td>\n",
       "      <td>2781.148430</td>\n",
       "      <td>1152.429405</td>\n",
       "      <td>2738.665311</td>\n",
       "      <td>2836.196979</td>\n",
       "      <td>402.692103</td>\n",
       "      <td>3006.129456</td>\n",
       "      <td>3468.656938</td>\n",
       "      <td>...</td>\n",
       "      <td>732.385043</td>\n",
       "      <td>3729.539192</td>\n",
       "      <td>8470.894648</td>\n",
       "      <td>12124.442908</td>\n",
       "      <td>1424.680381</td>\n",
       "      <td>2928.343463</td>\n",
       "      <td>172.325892</td>\n",
       "      <td>10754.212722</td>\n",
       "      <td>1647.866346</td>\n",
       "      <td>1839.937914</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CDM-03</th>\n",
       "      <td>2161.732859</td>\n",
       "      <td>7574.245304</td>\n",
       "      <td>1140.973842</td>\n",
       "      <td>2670.334041</td>\n",
       "      <td>947.491993</td>\n",
       "      <td>1754.851913</td>\n",
       "      <td>2656.107435</td>\n",
       "      <td>748.319502</td>\n",
       "      <td>3314.799316</td>\n",
       "      <td>2435.595034</td>\n",
       "      <td>...</td>\n",
       "      <td>636.640641</td>\n",
       "      <td>4280.785898</td>\n",
       "      <td>7546.503421</td>\n",
       "      <td>10815.066266</td>\n",
       "      <td>1151.643797</td>\n",
       "      <td>2941.350895</td>\n",
       "      <td>206.285794</td>\n",
       "      <td>15539.722287</td>\n",
       "      <td>1554.968091</td>\n",
       "      <td>1195.746277</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CDM-04</th>\n",
       "      <td>2239.702980</td>\n",
       "      <td>4317.867929</td>\n",
       "      <td>874.633847</td>\n",
       "      <td>3347.912090</td>\n",
       "      <td>1132.949168</td>\n",
       "      <td>2943.339362</td>\n",
       "      <td>2764.337759</td>\n",
       "      <td>1002.700035</td>\n",
       "      <td>4875.246903</td>\n",
       "      <td>2187.312267</td>\n",
       "      <td>...</td>\n",
       "      <td>665.798644</td>\n",
       "      <td>3011.738348</td>\n",
       "      <td>18418.973860</td>\n",
       "      <td>25238.498334</td>\n",
       "      <td>1352.699103</td>\n",
       "      <td>3141.259833</td>\n",
       "      <td>236.485857</td>\n",
       "      <td>14469.296219</td>\n",
       "      <td>1557.168414</td>\n",
       "      <td>1402.906870</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CDM-05</th>\n",
       "      <td>2259.277316</td>\n",
       "      <td>7996.845388</td>\n",
       "      <td>621.960584</td>\n",
       "      <td>2038.770678</td>\n",
       "      <td>1116.452214</td>\n",
       "      <td>2068.073885</td>\n",
       "      <td>2679.778347</td>\n",
       "      <td>694.486023</td>\n",
       "      <td>5341.242188</td>\n",
       "      <td>1038.066134</td>\n",
       "      <td>...</td>\n",
       "      <td>517.201616</td>\n",
       "      <td>1542.813887</td>\n",
       "      <td>7547.041150</td>\n",
       "      <td>9952.834504</td>\n",
       "      <td>1643.909953</td>\n",
       "      <td>2804.316979</td>\n",
       "      <td>121.608312</td>\n",
       "      <td>24476.236833</td>\n",
       "      <td>1386.041725</td>\n",
       "      <td>856.386246</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9_FM3814</th>\n",
       "      <td>1028.062029</td>\n",
       "      <td>504.984069</td>\n",
       "      <td>296.904314</td>\n",
       "      <td>1324.966343</td>\n",
       "      <td>594.631077</td>\n",
       "      <td>1042.866122</td>\n",
       "      <td>1189.262155</td>\n",
       "      <td>881.665996</td>\n",
       "      <td>2510.938699</td>\n",
       "      <td>1190.907054</td>\n",
       "      <td>...</td>\n",
       "      <td>294.436965</td>\n",
       "      <td>1612.001261</td>\n",
       "      <td>6499.819371</td>\n",
       "      <td>8215.449285</td>\n",
       "      <td>810.935328</td>\n",
       "      <td>1365.266374</td>\n",
       "      <td>79.777613</td>\n",
       "      <td>5512.057374</td>\n",
       "      <td>602.855574</td>\n",
       "      <td>514.853464</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9_FM3835</th>\n",
       "      <td>2409.192285</td>\n",
       "      <td>3476.351284</td>\n",
       "      <td>645.146122</td>\n",
       "      <td>2566.032320</td>\n",
       "      <td>1135.877571</td>\n",
       "      <td>2220.014099</td>\n",
       "      <td>2920.135078</td>\n",
       "      <td>948.316292</td>\n",
       "      <td>4946.120268</td>\n",
       "      <td>2095.512216</td>\n",
       "      <td>...</td>\n",
       "      <td>727.608408</td>\n",
       "      <td>2858.692590</td>\n",
       "      <td>14961.245780</td>\n",
       "      <td>22668.235730</td>\n",
       "      <td>1926.545374</td>\n",
       "      <td>3266.153299</td>\n",
       "      <td>219.090976</td>\n",
       "      <td>13718.652309</td>\n",
       "      <td>1979.903324</td>\n",
       "      <td>1537.679103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <td>3899.836861</td>\n",
       "      <td>6769.609285</td>\n",
       "      <td>364.500881</td>\n",
       "      <td>2700.962282</td>\n",
       "      <td>1292.419054</td>\n",
       "      <td>2023.571264</td>\n",
       "      <td>4314.873263</td>\n",
       "      <td>573.094306</td>\n",
       "      <td>8742.645029</td>\n",
       "      <td>991.356379</td>\n",
       "      <td>...</td>\n",
       "      <td>565.567739</td>\n",
       "      <td>1288.118158</td>\n",
       "      <td>4039.615960</td>\n",
       "      <td>5422.353816</td>\n",
       "      <td>2408.501398</td>\n",
       "      <td>5466.437993</td>\n",
       "      <td>167.734919</td>\n",
       "      <td>51606.443339</td>\n",
       "      <td>2848.267947</td>\n",
       "      <td>635.457288</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <td>5000.246936</td>\n",
       "      <td>4483.172769</td>\n",
       "      <td>725.767163</td>\n",
       "      <td>3340.019613</td>\n",
       "      <td>1848.423685</td>\n",
       "      <td>3522.625985</td>\n",
       "      <td>6262.653233</td>\n",
       "      <td>1956.496845</td>\n",
       "      <td>15095.770653</td>\n",
       "      <td>1151.538143</td>\n",
       "      <td>...</td>\n",
       "      <td>577.632402</td>\n",
       "      <td>2500.589300</td>\n",
       "      <td>6345.571432</td>\n",
       "      <td>6870.098920</td>\n",
       "      <td>2201.524783</td>\n",
       "      <td>5335.646395</td>\n",
       "      <td>294.406192</td>\n",
       "      <td>26368.919138</td>\n",
       "      <td>1525.135874</td>\n",
       "      <td>844.088639</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9_KO_AMP09</th>\n",
       "      <td>5165.570071</td>\n",
       "      <td>3740.122137</td>\n",
       "      <td>334.778822</td>\n",
       "      <td>3299.825635</td>\n",
       "      <td>1453.266232</td>\n",
       "      <td>2426.906644</td>\n",
       "      <td>5979.015460</td>\n",
       "      <td>537.180917</td>\n",
       "      <td>13581.084693</td>\n",
       "      <td>616.798803</td>\n",
       "      <td>...</td>\n",
       "      <td>612.961797</td>\n",
       "      <td>1467.655006</td>\n",
       "      <td>2466.235962</td>\n",
       "      <td>3140.589863</td>\n",
       "      <td>2244.648833</td>\n",
       "      <td>5742.080306</td>\n",
       "      <td>258.038691</td>\n",
       "      <td>54612.114262</td>\n",
       "      <td>2831.710836</td>\n",
       "      <td>518.955136</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1221 rows × 9231 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "Symbol               NOC2L        PERM1         AGRN         SDF4  \\\n",
       "CDM-01         2131.013236  1015.663855   752.970549  1719.732070   \n",
       "CDM-02         2026.624297  1562.900107  1527.597234  2781.148430   \n",
       "CDM-03         2161.732859  7574.245304  1140.973842  2670.334041   \n",
       "CDM-04         2239.702980  4317.867929   874.633847  3347.912090   \n",
       "CDM-05         2259.277316  7996.845388   621.960584  2038.770678   \n",
       "...                    ...          ...          ...          ...   \n",
       "9_FM3814       1028.062029   504.984069   296.904314  1324.966343   \n",
       "9_FM3835       2409.192285  3476.351284   645.146122  2566.032320   \n",
       "9_HL_VL_AMP08  3899.836861  6769.609285   364.500881  2700.962282   \n",
       "9_JE_VL_AMP05  5000.246936  4483.172769   725.767163  3340.019613   \n",
       "9_KO_AMP09     5165.570071  3740.122137   334.778822  3299.825635   \n",
       "\n",
       "Symbol              UBE2J2        ACAP3       INTS11         CPTP  \\\n",
       "CDM-01         1045.130646  1909.698828  2885.864644   505.324115   \n",
       "CDM-02         1152.429405  2738.665311  2836.196979   402.692103   \n",
       "CDM-03          947.491993  1754.851913  2656.107435   748.319502   \n",
       "CDM-04         1132.949168  2943.339362  2764.337759  1002.700035   \n",
       "CDM-05         1116.452214  2068.073885  2679.778347   694.486023   \n",
       "...                    ...          ...          ...          ...   \n",
       "9_FM3814        594.631077  1042.866122  1189.262155   881.665996   \n",
       "9_FM3835       1135.877571  2220.014099  2920.135078   948.316292   \n",
       "9_HL_VL_AMP08  1292.419054  2023.571264  4314.873263   573.094306   \n",
       "9_JE_VL_AMP05  1848.423685  3522.625985  6262.653233  1956.496845   \n",
       "9_KO_AMP09     1453.266232  2426.906644  5979.015460   537.180917   \n",
       "\n",
       "Symbol                 DVL1        MXRA8  ...      POFUT2      COL18A1  \\\n",
       "CDM-01          3567.989505  3157.335292  ...  660.808459  2386.810059   \n",
       "CDM-02          3006.129456  3468.656938  ...  732.385043  3729.539192   \n",
       "CDM-03          3314.799316  2435.595034  ...  636.640641  4280.785898   \n",
       "CDM-04          4875.246903  2187.312267  ...  665.798644  3011.738348   \n",
       "CDM-05          5341.242188  1038.066134  ...  517.201616  1542.813887   \n",
       "...                     ...          ...  ...         ...          ...   \n",
       "9_FM3814        2510.938699  1190.907054  ...  294.436965  1612.001261   \n",
       "9_FM3835        4946.120268  2095.512216  ...  727.608408  2858.692590   \n",
       "9_HL_VL_AMP08   8742.645029   991.356379  ...  565.567739  1288.118158   \n",
       "9_JE_VL_AMP05  15095.770653  1151.538143  ...  577.632402  2500.589300   \n",
       "9_KO_AMP09     13581.084693   616.798803  ...  612.961797  1467.655006   \n",
       "\n",
       "Symbol               COL6A1        COL6A2          LSS       MCM3AP  \\\n",
       "CDM-01          4548.543992   5520.321137  1261.429430  2815.645909   \n",
       "CDM-02          8470.894648  12124.442908  1424.680381  2928.343463   \n",
       "CDM-03          7546.503421  10815.066266  1151.643797  2941.350895   \n",
       "CDM-04         18418.973860  25238.498334  1352.699103  3141.259833   \n",
       "CDM-05          7547.041150   9952.834504  1643.909953  2804.316979   \n",
       "...                     ...           ...          ...          ...   \n",
       "9_FM3814        6499.819371   8215.449285   810.935328  1365.266374   \n",
       "9_FM3835       14961.245780  22668.235730  1926.545374  3266.153299   \n",
       "9_HL_VL_AMP08   4039.615960   5422.353816  2408.501398  5466.437993   \n",
       "9_JE_VL_AMP05   6345.571432   6870.098920  2201.524783  5335.646395   \n",
       "9_KO_AMP09      2466.235962   3140.589863  2244.648833  5742.080306   \n",
       "\n",
       "Symbol               YBEY          PCNT        DIP2A        PRMT2  \n",
       "CDM-01         186.831993  16820.521951  1587.444988  1669.575830  \n",
       "CDM-02         172.325892  10754.212722  1647.866346  1839.937914  \n",
       "CDM-03         206.285794  15539.722287  1554.968091  1195.746277  \n",
       "CDM-04         236.485857  14469.296219  1557.168414  1402.906870  \n",
       "CDM-05         121.608312  24476.236833  1386.041725   856.386246  \n",
       "...                   ...           ...          ...          ...  \n",
       "9_FM3814        79.777613   5512.057374   602.855574   514.853464  \n",
       "9_FM3835       219.090976  13718.652309  1979.903324  1537.679103  \n",
       "9_HL_VL_AMP08  167.734919  51606.443339  2848.267947   635.457288  \n",
       "9_JE_VL_AMP05  294.406192  26368.919138  1525.135874   844.088639  \n",
       "9_KO_AMP09     258.038691  54612.114262  2831.710836   518.955136  \n",
       "\n",
       "[1221 rows x 9231 columns]"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merge_H = merge_L_combat_tmm.set_index('Symbol').T.fillna(0)\n",
    "\n",
    "merge_H.to_csv('Integration data/All_muscle_H_combatseq_tmm.csv')\n",
    "merge_H"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "base",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.13"
  },
  "orig_nbformat": 4,
  "vscode": {
   "interpreter": {
    "hash": "703384a5d51203336cae96812a329c25b622e8ff013b63f0dd02bc2f383650b0"
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}