cBioPortal

cBioPortal is a centralized portal for exploring and analyzing published cancer genomics and clinical datasets. The portal aggregates a curated, non-redundant collection of cohort studies — from large public resources (TCGA, ICGC, CPTAC) to institution-specific clinical sequencing cohorts (e.g., MSK-IMPACT), clinical trials, pediatric consortia and cell-line resources — and links each dataset to its underlying publications. The site exposes sample counts and available data types for every study and provides direct links to download study-level data, supporting reproducible research and cross-study comparisons. The platform is designed for both high-level cohort queries and detailed patient-centric inspection. Users can filter studies by tumor type, study cohort and available data types, then visualize and analyze selected collections. For individual cases the portal exposes a patient view that combines clinical annotations with molecular data from that sample. For cohort analyses it provides tools to compare alteration frequencies, assess co-occurrence and mutual exclusivity, and relate molecular features to clinical endpoints and phenotypes. Every study entry includes provenance information (publication citations and authors) so findings can be traced back to the original research. Typical use-cases span basic, translational and clinical research. Translational scientists use the portal to compare the prevalence of specific gene alterations (for example BRCA1/2, TP53, or pathway-level events) across tumor types and cohorts to prioritize targets or stratify trial eligibility. Clinical researchers and molecular tumor boards use the patient view to inspect an individual tumor’s genomic profile in the context of curated cohorts and published evidence. Bioinformaticians and data scientists download cohort-level matrices and sample annotations to run custom statistical analyses, machine-learning models or to integrate cBioPortal cohorts with in-house datasets. Educators and students use the portal to illustrate pan-cancer patterns and to follow examples from linked publications. cBioPortal integrates a wide spectrum of datasets and study types: large pan-cancer projects (TCGA PanCancer Atlas, pan-cancer whole-genome analyses), institutional clinical sequencing cohorts (MSK-IMPACT and associated cohorts), proteogenomic and CPTAC studies, pediatric consortia (TARGET, DKFZ), cell-line collections (Cancer Cell Line Encyclopedia, NCI-60), clinical trial cohorts (basket trials such as SUMMIT), patient-derived models and circulating tumor DNA studies. The portal makes it straightforward to browse by tumor type (breast, lung, colorectal, glioma, hematologic malignancies and many rarer entities), to select specific published cohorts and to see the supporting citations and sample counts for each dataset. For groups that need to work with private clinical data, the portal supports local installations: teams can run private or institutional instances and — if desired — add their installation to the public map. The portal also maintains community-facing resources such as a newsletter and documentation to keep researchers informed about new datasets, feature updates and notable analyses. Overall, cBioPortal acts as a bridge between published cancer genomics data and practical analysis needs, lowering the barrier to cross-study comparison, cohort discovery and reproducible downstream research.