Table 1 Public omics data and clinical resources
From: An integrated clinical and genomic information system for cancer precision medicine
Category | Resource | Comments |
|---|---|---|
Gene | Hugo symbol (http://www.genenames.org) | Gene symbol mapping |
Entrez genes (https://www.ncbi.nlm.nih.gov/gene) | Gene model | |
Protein | Uniprot (http://www.uniprot.org) | Protein model |
Pfam (http://pfam.xfam.org) | Protein domains | |
Cancer gene variants | COSMIC cancer gene census [10] | Catalogue of Somatic Mutations in Cancer |
Personalized Cancer Medicine Knowledge Base [13] | MD Anderson Cancer Center | |
Cancer omics data | The Cancer Genome Atlas (TCGA; http://cancergenome.nih.gov) | Somatic mutations RNA expressions Copy Number Variations Clinical information |
Drug and clinical trials | MyCancerGenome [12] | Vanderbilt-Ingram Cancer Center |
OncoKB [11] | Memorial Sloan Kettering Cancer Center | |
VarDrugPub [17] | In-house database for mutation-gene-drug relations mined from all the PubMed articles | |
IntOGen [15] | Anticancer drugs database | |
Handbook of targeted cancer therapy [16] | More than 120 targeted therapy agents for which clinical trial data are available | |
The New England Journal of Medicine | Manual search · Key words: breast | lung | glio & cancer & survival & genetic profile · Searching option: past 10 years |