06-predict-gene-modulation-targets.ipynb

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   "source": [
    "# Predict expression modulation targets\n",
    "\n",
    "Cameo provides algorithms to search for genes or reactions that can be over or down regulated in order to achieve a given biological objective."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
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     "metadata": {},
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   ],
   "source": [
    "from cameo import models"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Load the E. coli core model."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "model = models.bigg.e_coli_core"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Flux Scanning based on Enforced Objective Flux"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from cameo.strain_design.deterministic.flux_variability_based import FSEOF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
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   "source": [
    "fseof = FSEOF(model)"
   ]
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   "execution_count": 5,
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       "\n",
       "<strong>Model:</strong> e_coli_core</br>\n",
       "<strong>Enforced objective:</strong> EX_succ_e</br>\n",
       "<strong>Primary objective:</strong> Maximize\n",
       "-1.0*BIOMASS_Ecoli_core_w_GAM_reverse_712e5 + 1.0*BIOMASS_Ecoli_core_w_GAM</br>\n",
       "<br>\n",
       "<strong>Reaction fluxes</strong><br><br>\n",
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>1</th>\n",
       "      <th>2</th>\n",
       "      <th>3</th>\n",
       "      <th>4</th>\n",
       "      <th>5</th>\n",
       "      <th>6</th>\n",
       "      <th>7</th>\n",
       "      <th>8</th>\n",
       "      <th>9</th>\n",
       "      <th>10</th>\n",
       "    </tr>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ADK1</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.410338</td>\n",
       "      <td>1.527283</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENO</th>\n",
       "      <td>15.238892</td>\n",
       "      <td>15.761645</td>\n",
       "      <td>16.212407</td>\n",
       "      <td>16.577535</td>\n",
       "      <td>16.942662</td>\n",
       "      <td>17.307790</td>\n",
       "      <td>17.704415</td>\n",
       "      <td>18.602292</td>\n",
       "      <td>19.293292</td>\n",
       "      <td>19.628048</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>FBA</th>\n",
       "      <td>7.756941</td>\n",
       "      <td>8.036499</td>\n",
       "      <td>8.242515</td>\n",
       "      <td>8.361048</td>\n",
       "      <td>8.479582</td>\n",
       "      <td>8.598115</td>\n",
       "      <td>8.747793</td>\n",
       "      <td>9.393102</td>\n",
       "      <td>9.830787</td>\n",
       "      <td>9.910940</td>\n",
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       "    <tr>\n",
       "      <th>FRD7</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.453235</td>\n",
       "      <td>3.175302</td>\n",
       "      <td>4.897369</td>\n",
       "      <td>6.586703</td>\n",
       "      <td>7.755141</td>\n",
       "      <td>9.127842</td>\n",
       "      <td>10.852285</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GAPD</th>\n",
       "      <td>16.431132</td>\n",
       "      <td>16.838737</td>\n",
       "      <td>17.173618</td>\n",
       "      <td>17.421989</td>\n",
       "      <td>17.670359</td>\n",
       "      <td>17.918730</td>\n",
       "      <td>18.198431</td>\n",
       "      <td>18.976723</td>\n",
       "      <td>19.547784</td>\n",
       "      <td>19.761991</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ICL</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.386057</td>\n",
       "      <td>1.231342</td>\n",
       "      <td>2.076627</td>\n",
       "      <td>2.921912</td>\n",
       "      <td>3.735322</td>\n",
       "      <td>4.041459</td>\n",
       "      <td>4.143333</td>\n",
       "      <td>3.893465</td>\n",
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       "    <tr>\n",
       "      <th>MALS</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.386057</td>\n",
       "      <td>1.231342</td>\n",
       "      <td>2.076627</td>\n",
       "      <td>2.921912</td>\n",
       "      <td>3.735322</td>\n",
       "      <td>4.041459</td>\n",
       "      <td>4.143333</td>\n",
       "      <td>3.893465</td>\n",
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       "    <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",
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       "    <tr>\n",
       "      <th>PGM</th>\n",
       "      <td>-15.238892</td>\n",
       "      <td>-15.761645</td>\n",
       "      <td>-16.212407</td>\n",
       "      <td>-16.577535</td>\n",
       "      <td>-16.942662</td>\n",
       "      <td>-17.307790</td>\n",
       "      <td>-17.704415</td>\n",
       "      <td>-18.602292</td>\n",
       "      <td>-19.293292</td>\n",
       "      <td>-19.628048</td>\n",
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       "    <tr>\n",
       "      <th>PPC</th>\n",
       "      <td>3.758320</td>\n",
       "      <td>5.012330</td>\n",
       "      <td>5.878875</td>\n",
       "      <td>6.284516</td>\n",
       "      <td>6.690157</td>\n",
       "      <td>7.095799</td>\n",
       "      <td>7.532996</td>\n",
       "      <td>8.472367</td>\n",
       "      <td>9.615323</td>\n",
       "      <td>11.108854</td>\n",
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       "      <th>PPS</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.410338</td>\n",
       "      <td>1.527283</td>\n",
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       "    <tr>\n",
       "      <th>SUCCt3</th>\n",
       "      <td>1.474575</td>\n",
       "      <td>2.949150</td>\n",
       "      <td>4.423725</td>\n",
       "      <td>5.898300</td>\n",
       "      <td>7.372875</td>\n",
       "      <td>8.847450</td>\n",
       "      <td>10.322025</td>\n",
       "      <td>11.796600</td>\n",
       "      <td>13.271175</td>\n",
       "      <td>14.745750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THD2</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.119674</td>\n",
       "      <td>2.143848</td>\n",
       "      <td>2.916807</td>\n",
       "      <td>1.535161</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TPI</th>\n",
       "      <td>7.756941</td>\n",
       "      <td>8.036499</td>\n",
       "      <td>8.242515</td>\n",
       "      <td>8.361048</td>\n",
       "      <td>8.479582</td>\n",
       "      <td>8.598115</td>\n",
       "      <td>8.747793</td>\n",
       "      <td>9.393102</td>\n",
       "      <td>9.830787</td>\n",
       "      <td>9.910940</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_succ_e</th>\n",
       "      <td>1.474575</td>\n",
       "      <td>2.949150</td>\n",
       "      <td>4.423725</td>\n",
       "      <td>5.898300</td>\n",
       "      <td>7.372875</td>\n",
       "      <td>8.847450</td>\n",
       "      <td>10.322025</td>\n",
       "      <td>11.796600</td>\n",
       "      <td>13.271175</td>\n",
       "      <td>14.745750</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>18 rows × 10 columns</p>\n",
       "</div>\n"
      ],
      "text/plain": [
       "<cameo.strain_design.deterministic.flux_variability_based.FSEOFResult at 0x119526a58>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "fseof.run(target=model.reactions.EX_succ_e)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Differential flux variability analysis\n",
    "\n",
    "Compares flux ranges of a reference model to a set of models that have been parameterized to lie on a grid of evenly spaced points in the n-dimensional production envelope (n being the number of reaction bounds to be varied)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from cameo.flux_analysis.analysis import phenotypic_phase_plane\n",
    "from cameo.strain_design.deterministic import DifferentialFVA"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Succinate production"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The production envelope looks like this."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
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   "source": [
    "production_envelope = phenotypic_phase_plane(model, \n",
    "                                             variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],\n",
    "                                             objective=model.metabolites.succ_e)\n",
    "production_envelope.plot(height=400)"
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Set up a model that represents a reference state (in this case a model with a constrained growth rate)."
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   "execution_count": 8,
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    "model.reactions.EX_o2_e.lower_bound = 0\n",
    "reference_model = model.copy()\n",
    "biomass_rxn = reference_model.reactions.BIOMASS_Ecoli_core_w_GAM\n",
    "biomass_rxn.lower_bound = 0.\n",
    "target = reference_model.metabolites.succ_e"
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   "source": [
    "Set up the differential flux variability analysis strain design method."
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   "execution_count": 9,
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   "source": [
    "diffFVA = DifferentialFVA(design_space_model=model,\n",
    "                          reference_model=reference_model,\n",
    "                          objective=target,\n",
    "                          variables=[biomass_rxn],\n",
    "                          normalize_ranges_by=biomass_rxn,\n",
    "                          points=10)"
   ]
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  {
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   "metadata": {},
   "source": [
    "Run differential flux variability analysis (only on the surface of the production envelope)"
   ]
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   "execution_count": 10,
   "metadata": {
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     "text": [
      "CPU times: user 1.49 s, sys: 32.3 ms, total: 1.52 s\n",
      "Wall time: 2.16 s\n"
     ]
    },
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   "source": [
    "%time result = diffFVA.run(surface_only=True)\n",
    "result.plot()"
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  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
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       "      <th></th>\n",
       "      <th>upper_bound</th>\n",
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       "      <th>normalized_gaps</th>\n",
       "      <th>KO</th>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SUCDi</th>\n",
       "      <td>990.126</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SUCOAS</th>\n",
       "      <td>0</td>\n",
       "      <td>-1.88738e-14</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TALA</th>\n",
       "      <td>-0.0168296</td>\n",
       "      <td>-0.0168296</td>\n",
       "      <td>0</td>\n",
       "      <td>-0.141033</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THD2</th>\n",
       "      <td>1.61298</td>\n",
       "      <td>1.61298</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT1</th>\n",
       "      <td>-0.0168296</td>\n",
       "      <td>-0.0168296</td>\n",
       "      <td>0</td>\n",
       "      <td>-0.141033</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT2</th>\n",
       "      <td>-0.0507897</td>\n",
       "      <td>-0.0507897</td>\n",
       "      <td>0</td>\n",
       "      <td>-0.425623</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TPI</th>\n",
       "      <td>9.90643</td>\n",
       "      <td>9.90643</td>\n",
       "      <td>0</td>\n",
       "      <td>95.3064</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>76 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        upper_bound  lower_bound gaps normalized_gaps     KO flux_reversal  \\\n",
       "ACALD  -9.10733e-16 -9.10733e-16    0               0  False         False   \n",
       "ACALDt            0            0    0               0  False         False   \n",
       "ACKr       -8.69634     -8.69634    0          82.443  False         False   \n",
       "ACONTa     0.101495     0.101495    0               0  False         False   \n",
       "ACONTb     0.101495     0.101495    0               0  False         False   \n",
       "ACt2r      -8.69634     -8.69634    0          82.443  False         False   \n",
       "ADK1       0.583116     0.583116    0               0  False         False   \n",
       "...             ...          ...  ...             ...    ...           ...   \n",
       "SUCDi       990.126            0    0               0  False         False   \n",
       "SUCOAS            0 -1.88738e-14    0               0  False         False   \n",
       "TALA     -0.0168296   -0.0168296    0       -0.141033  False         False   \n",
       "THD2        1.61298      1.61298    0               0  False         False   \n",
       "TKT1     -0.0168296   -0.0168296    0       -0.141033  False         False   \n",
       "TKT2     -0.0507897   -0.0507897    0       -0.425623  False         False   \n",
       "TPI         9.90643      9.90643    0         95.3064  False         False   \n",
       "\n",
       "       suddenly_essential  \n",
       "ACALD                True  \n",
       "ACALDt               True  \n",
       "ACKr                 True  \n",
       "ACONTa              False  \n",
       "ACONTb              False  \n",
       "ACt2r                True  \n",
       "ADK1                False  \n",
       "...                   ...  \n",
       "SUCDi               False  \n",
       "SUCOAS               True  \n",
       "TALA                 True  \n",
       "THD2                False  \n",
       "TKT1                 True  \n",
       "TKT2                 True  \n",
       "TPI                 False  \n",
       "\n",
       "[76 rows x 7 columns]"
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