TCGA

The Cancer Genome Atlas (TCGA), 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.

  • TCGA Pan-Cancer Atlas 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 from Genomic Data Commons 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 in the UCSC RNA-seq Recompute Compendium 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.

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

Please see our help page on how to choose between these different versions of the TCGA data

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

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