README.md

BioGRID

• consider this as a milestone on my learning journey to undersand synthetic lethality.

• as an initial search for synthetic lethality I recommend using the STRING "Geneset by Pathway / Process / Disease / Publication" option from the initial search screen.

  • use a search terms similar to "TP53 synthetic lethality"
  • this will return a list of publications that can then be used to generate the graph network

• in many respects when querying for synthetic lethality / negative genetic interactor genes the most valuable column is the "Publication Source" (I think this mapped to around 7 PubMed references total)

• core files for TP53

  • biogrid-synthetic-lethality-filtered-cols.csv
  • biogrid-tp53-negative-genetic-filtered-cols.csv

• core files for RB1

  • stay tuned

CITATION:

Oughtred R, Rust J, Chang C, Breitkreutz BJ, Stark C, Willems A, Boucher L, Leung G, Kolas N, Zhang F, Dolma S, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 2021 Jan;30(1):187-200. doi: 10.1002/pro.3978. Epub 2020 Nov 23. PMID: 33070389; PMCID: PMC7737760.