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TCGA / NCI Genomic Data Commons
The reference atlas of cancer genomes that most cancer biology since 2008 is built on.
Also called: TCGAThe Cancer Genome AtlasGDCGenomic Data CommonsGDC Data PortalTCGA PanCanAtlas
· 1 more · Fewer names
Pan-Cancer Atlas
Overview
The NCI Genomic Data Commons hosts The Cancer Genome Atlas, multi-omic data on more than 11,000 tumours across 33 cancer types, together with TARGET, CPTAC and other programmes. Mutations, copy number, RNA, methylation, protein and clinical data are harmonised into one portal, which is why it has become the training set for most cancer machine learning and the reference atlas that most cancer biology since 2008 is built on. The NCI maintains it; processed data are open and raw sequence is under controlled access. On OnCo it is tied to Whole-exome and whole-genome sequencing and DNA methylation profiling, and it is cited by the bottleneck Data silos, the paper TCGA Pan-Cancer Atlas, the Virtual cell roadmap and the Drug discovery roadmap.
Holds
Multi-omic data on >11,000 tumours across 33 cancer types (TCGA) plus TARGET, CPTAC, and others.
Licence
Open (controlled access for raw sequence)
Maintainer
NCI
Dataset registry
Size: More than 11,000 tumours across 33 cancer types (TCGA) plus TARGET and CPTAC
Access: controlled
Consent and reuse: Open for processed data; dbGaP authorisation for raw sequence and germline.
All datasets and the models trained on them →methodsNucleic Acids Research 20204,312 citations
Li 2020: TIMER2.0 for analysis of tumour-infiltrating immune cells
TIMER2.0 is one of the most used tools in cancer immunogenomics and its multi-algorithm design is a reminder that computational immune cell estimates are model-dependent and should be cross-checked.
basicCell 20182,098 citations
TCGA Pan-Cancer Atlas: 10,000 tumours across 33 cancer types, classified by molecular features
Cancers are defined as much by the tissue they come from as by the mutations they carry, which is why the same drug can work in one organ and fail in another with the same mutation. TCGA is the shared public dataset behind most modern biomarkers and target discovery.
methodsCancer Research 20174,751 citations
Li 2017: TIMER, a web server for estimating immune cells in tumour genomic data
TIMER made immune infiltration analysis accessible to any group with tumour expression data, which is why it is cited so heavily; it is a standard first step in linking a gene or mutation to the immune state of a cancer.
Similar pages
- TermData use agreements and consent for research use
Shares TCGA open versus controlled data tiers, Controlled-access genomic data (dbGaP, EGA), Cancer AI vocabulary (CanSim terms map).
- CollectionCPTAC (Clinical Proteomic Tumor Analysis Consortium)
Shares Link single-cell and spatial tumour atlases to clinical outcomes, Drug discovery roadmap: screening in mice → maps of dependency → designing in silico, Data silos, Cancer AI vocabulary (CanSim terms map).
- TermAnalytical databases as a data catalogue (DuckDB, PostgreSQL)
Shares TCGA barcode, Cancer AI vocabulary (CanSim terms map).
- CollectionCZ CELLxGENE / Human Cell Atlas
Shares Link single-cell and spatial tumour atlases to clinical outcomes, Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Cancer AI vocabulary (CanSim terms map).
- TermLocal-only language models over patient data (privacy by architecture)
Shares Controlled-access genomic data (dbGaP, EGA), Cancer AI vocabulary (CanSim terms map).
- TermDeep mass-spectrometry proteome (CPTAC)
Shares Reverse-phase protein array (RPPA), Cancer AI vocabulary (CanSim terms map).
- CompanyVevo Therapeutics
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Drug discovery roadmap: screening in mice → maps of dependency → designing in silico.
- CollectioncBioPortal for Cancer Genomics
Shares A global rapid tissue donation network for metastatic disease, Data silos, Whole-exome & whole-genome sequencing.
technologies
institutions
terms
roadmaps
ideas
bottlenecks
key papers
Open-source projects
All open source in oncology →Open-source projects that are the code behind this collection or publish it, from OnCo's own catalogue: licence and last activity as the repository reported them on the day of the fetch. Listing is not endorsement; check the licence before reuse and the validation before clinical use.
A Bioconductor package that queries, downloads and prepares TCGA and other GDC data for analysis in R.
The command-line client for downloading from the NCI Genomic Data Commons, home of TCGA, TARGET and CPTAC genomics.
The schema that defines every entity and field in the Genomic Data Commons.
Curated, ready-to-analyse TCGA multi-assay data as Bioconductor objects.