Drug-gene interaction database scraper for rare kidney cancer treatment research proposals
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Kidney Bean P1RCC 2018.pdf
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README.md
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c2.all.v6.1.symbols.gmt.txt
c2_nodups.txt
class_to_gene.py
drug_to_effect.py
geneName.txt
gene_categories.json
gene_to_drug.py
gene_to_graph.py
graph_drug_risk.py
gsea.ipynb
gsea.py

README.md

KidneyBean

is a colab aimed at moving the needle on p1RCC (kidney cancer)

Get started

To get this codebase,

  1. install git (e.g. apt-get install git)
  2. git clone https://github.com/SVAI/KidneyBean.git

What this does

  1. Given a .vcf (difference between cancer and non-cancer genome)
  2. Find the class of genes most representative of the disease
  3. Select the drugs known to interact with those genes
  4. Determine reported adverse effects associated with those drugs
  5. Recommend drug research targets

How we recommend drug research targets

Given a gene enrichment set over the variants called between a type 1 renal papilary carcinoma tumor, we extract drugs from gdidb.org which are known to interact with these genes. Furthermore, we extract risk profiles for the selected drugs from the FDA's adverse event reporting database. Sorting the dgi-suggested genes by these risk profiles, we suggest research candidates.