UCSC XenaXena

Explore TCGA, GDC, and other public cancer genomics resources

Mary Goldman6 March 2019

Discover new trends and validate your findings with 1500+ datasets and 50+ cancer types.

We provide interactive online visualization of seminal cancer genomics datasets, including data from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), Genomic Data Commons (GDC), and UCSC RNA-seq compendium.

Xena supports virtually any functional genomics data, including SNVs, INDELs, large structural variants, copy number variation, gene-, transcript-, exon-, miRNA-, LncRNA-, protein-expressions, DNA methylation, ATAC-seq signals, phenotypic annotations, and higher-level derived genomic parameters.

Public Xena Hubs Samples Data Types
TCGA 12,470 copy number, gene-, exon-, miRNA-, and protein-expression, somatic mutation, DNA methylation, survival, and clinical data
Pan-Cancer Atlas 12,591 copy number, gene-, miRNA-, and protein-expression, somatic mutation, DNA methylation, molecular subtypes, multiple curated survival endpoints
ICGC 17,697 copy number, gene expression, somatic mutation
UCSC RNA-seq compendium 19,131 TCGA, TARGET, and GTEx gene- and transcript-expression
GDC 20,157 TCGA and TARGET copy number, somatic mutations, gene- and miRNA-expression, DNA methylation, overall survival, and clinical data
TCGA ATAC-seq 404  ATAC-seq peak signal
Collected from the literature * various, study-dependent

Table: Summary of data hosted on Public Xena Hubs as of October 26, 2018.

TCGA

TCGA is our most used data resource. We host serveral 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 uniformaly 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.

More studies

  • UCSC RNA-seq recompute compendium TCGA, TARGET and GTEx RNA-seq data are uniformly re-aligned to hg38 genome, and re-processed using RSEM and Kallisto methods with gencode v23 annotations to generate expression estimates for ~60,000 genes and ~200,000 transcripts, including many LncRNAs. Xena hosts and displays gene and transcript expression results of this analysis.

  • ICGC International Cancer Genome Consortium (ICGC) goal is to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe. It includes TCGA data (U.S.A.) plus data contributed by groups from other countries in the International Cancer Genome Consortium. The resource has publically-accessible non-coding somatic mutation data from non-TCGA samples.

  • MET500 Xena displays gene expression data from the metastatic cancer study published in Robinson et al 2017 Integrative clinical genomics of metastatic cancer.

  • CCLE Cancer Cell Line Encyclopedia. Detailed genetic and pharmacologic characterization of a large panel (~1100) of human cancer cell lines.

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