Introduction to UCSC Xena

About this Class

UCSC Xena ( xena.ucscedu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as well as the GDC, PCAWG, and ICGC; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data modality, including SNPs, INDELs, large structural variants, CNV, gene and other types of expression, DNA methylation, clinical and phenotypic annotations. Browser features include the high performance Visual Spreadsheet, dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, charts, statistical analyses, genomic signatures, and live bookmarks. Researchers can securely view their own analysis results side-by-side with the data already in Xena, enabling insight and discovery between public and private data. Integration occurs only within the Xena Browser, ensuring pre-publication data remains private. Xena can help you answer questions like: * Is over-expression of geneA associated with lower survival? * Is geneB differentially expressed in tumor vs normal? * Do my subgroups have differential survival? * What is the relationship between expression, mutation, copy number, etc for these genes? This webinar will include a live demonstration of Xena. Please bring a laptop with either Chrome or Firefox installed to follow along. The ITCR Program is a trans-NCI program supporting investigator-initiated, research-driven informatics technology development spanning all aspects of cancer research. The ITCR Program funds tools that support the analysis of -omics, imaging, and clinical data, as well as network biology and data standards. All of the tools are free for use by academic and non-profit researchers. Access to tools, code repositories, and introductory videos are available on the website itcr.cancergov/