Introduction to UCSC Xena: a Tool for Multiomic Data and Associated Clinical and Phenotypic Annotations

About this Class

UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Consortium; a total of more than 1,500 datasets across 50 cancer types. You can use the same visualizations to view your own data privately and securely in UCSC Xena.

UCSC Xena supports virtually any type of functional genomics data modality, including:

• single nucleotide polymorphisms.
• insertions and deletions.
• large structural variants.
• copy number variation.
• gene and other types of expression.
• DNA methylation.
• clinical and phenotypic annotations.

Browser features of UCSC Xena include:

• high-performance visual spreadsheet.
• dynamic Kaplan-Meier survival analysis.
• genome-wide differential gene expression analysis.
• genome-wide gene set enrichment analysis.
• powerful filtering and subgrouping.
• charts.
• statistical analyses.
• genomic signatures.
• live bookmarks.

UCSC Xena can help you answer these questions:

• Is over-expression of this gene associated with lower survival in these two cancer types?
• Is this gene differentially expressed in TCGA tumor vs GTEx normal?
• What are the most differentially expressed genes for the subgroups I just made?