PanCanAtlas Publications
The Pan-Cancer Atlas (PanCanAtlas) initiative aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset.
Program Description
The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer Atlas initiative compares the 33 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.
Data in the GDC
- Download the GDC Manifest File (Open Access)
- Download the GDC Manifest File (Controlled Access)
Supplemental Data
- RNA (Final) - EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
- RPPA (Final) - TCGA-RPPA-pancan-clean.txt
- DNA Methylation (450K Only) - jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv
- DNA Methylation (Merged 27K+450K Only) - jhu-usc.edu_PANCAN_merged_HumanMethylation27_HumanMethylation450.betaValue_whitelisted.tsv
- miRNA (Batch Effects Normalized miRNA data)
- Sample List - PanCanAtlas_miRNA_sample_information_list.txt
- Protocol Platform - pancanMiRs_EBadjOnProtocolPlatformWithoutRepsWithUnCorrectMiRs_08_04_16.csv
- Copy Number - broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.seg
- ABSOLUTE-annotated MAF - TCGA_consolidated.abs_mafs_truncated.fixed.txt.gz
- ABSOLUTE-annotated seg file - TCGA_mastercalls.abs_segtabs.fixed.txt
- ABSOLUTE purity/ploidy file - TCGA_mastercalls.abs_tables_JSedit.fixed.txt
- Mutations - mc3.v0.2.8.PUBLIC.maf.gz
- TCGA-Clinical Data Resource (CDR) Outcome* - TCGA-CDR-SupplementalTableS1.xlsx
- A curated resource of the clinical annotations for TCGA data and provides recommendations for use of clinical endpoints
- *It is strongly recommended that this file be used for clinical elements and survival outcome data first; more details please see the TCGA-CDR paper.
- Clinical with Follow-up - clinical_PANCAN_patient_with_followup.tsv
- Merged Sample Quality Annotations - merged_sample_quality_annotations.tsv
- PARADIGM Pathway Inference Matrix - merge_merged_reals.tar.gz
Additional Resources
- ISB-CGC PanCancer Atlas BigQuery Tables (link is external) Institute for Systems Biology - This resource mirrors the above PanCancer Atlas data files as Google BigQuery tables. Using SQL database querying, answer questions and access your data of interest, without any downloads. Uniform annotations are provided, to ease combining data from different platforms, such as DNA mutation status and RNA expression levels. Includes extensive documentation and examples.
- Broad Institute FireCloud (link is external) The Broad Institute
- cBioPortal for Cancer Genomics (link is external) Memorial Sloan-Kettering Cancer Center
- Next-Generation Clustered Heat Maps (link is external) MD Anderson Cancer Center
Instructions for Data Download
Open Access Data
- Download the appropriate manifest file from the publication page
- Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
- GDC DTT (Download, User's Guide)
- GDC API (User’s Guide)
Controlled Access Data
- Download the appropriate manifest file from the publication page
- Download a token from the GDC Data Portal
- GDC Data Portal (Launch, User’s Guide)
- Use the manifest file and token to download data using the GDC DTT or the GDC API
- GDC DTT (Download, User’s Guide)
- GDC API (User’s Guide)
For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.