Skip to main content

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