cbioportal-database

You query cancer genomics data from cBioPortal by calling REST API endpoints like /studies, /molecular-profiles, and /clinical-data/fetch to retrieve mutations, CNAs, expression, and clinical variables across TCGA, GENIE, and other cohorts.

Retrieving TP53 mutation and survival data from TCGA involves querying molecular profiles for mutation data and integrating clinical attributes via the REST API, combining gene symbol resolution with sample-list handling to link genomic alterations to survival outcomes.

Yes, you can perform pan-study queries to compare mutation frequencies, CNAs, and survival across TCGA, GENIE, and other cohorts by fetching and integrating molecular profile data and clinical attributes from multiple cBioPortal studies.

Yes, clinical-data integration supports survival and treatment-outcome associations by fetching clinical attributes through the /clinical-data/fetch endpoint and linking them with molecular alterations like mutations and CNAs for correlative analysis.

Gene symbol resolution maps standard gene names to internal IDs for querying molecular profiles, while sample-list handling manages which tumor samples are included when fetching mutation, CNA, or expression data from a given cBioPortal study.

Limitations include variability in clinical attribute coverage across TCGA, GENIE, and other cohorts, which can constrain pan-study survival analysis when clinical data fields differ or are incomplete for certain studies fetched via the REST API.