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  1. Overview of public data

TCGA

Last updated 3 years ago

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, a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), has generated comprehensive, multi-dimensional maps of the key genomic changes in 33 types of cancer. The TCGA dataset, describing tumor tissue and matched normal tissues from more than 11,000 patients, is publicly available and has been used widely by the research community. The data have contributed to more than a thousand studies of cancer by independent researchers and to the TCGA research network publications.

TCGA is our most used data resource. We host several versions of the TCGA data.

  • As its concluding project, The Cancer Genome Atlas (TCGA) Research Network completes the most comprehensive cross-cancer analysis to date: The Pan-Cancer Atlas. Xena displays the curated genomics and clinical data generated by the Pan-Cancer Atlas consortium working groups.

  • TCGA data uniformly re-analyzed at GDC using the latest Human Genome Assembly hg38. We download all open-access tier data from GDC, compile individual files into datasets organized by cohorts (33 individual tumor cohorts as well as a Pancan cohort. Xena displays the compiled datasets.

  • TCGA data has been co-analyzed with GTEx data using the UCSC bioinformatic pipeline (TOIL RNA-seq) and can be used to compare tumor vs normal gene and transcript expression from the matching tissue of origin. Xena hosts gene and transcript expression results of the UCSC RNA-seq recompute compendium.

  • Data generated and published by TCGA Research Network before the Pan-Cancer Atlas publications. Xena displays the level-3 data.

This paper helps clarify the differences between the Legacy TCGA data and the TCGA data on the GDC:

The Cancer Genome Atlas (TCGA)
TCGA Pan-Cancer Atlas
TCGA data from Genomic Data Commons
TCGA data in the UCSC RNA-seq Recompute Compendium
Legacy TCGA data
Please see our help page on how to choose between these different versions of the TCGA data
LogoBefore and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons | NCI Genomic Data CommonsNCIGDC_Updates