Abstract 250: UCSC Xena for the visualization and analysis of cancer genomics data

UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Data is kept on the researcher9s computer (we support Mac, Windows, and Linux) and is never uploaded to public servers. Questions Xena can help you answer: * Is overexpression of this gene associated with lower/higher survival? * Do my two subgroups have differential survival? * Is this gene differentially expressed in tumor vs normal samples? * What is the relationship between mutation, copy number, expression, etc for this gene? Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, GDC, PCAWG, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data: SNPs, INDELs, copy number variation, gene expression, ATAC-seq, DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotypes, subtype classifications and biomarkers. All of our data is available for download via python or R APIs, or URL links. We show multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. Other visualizations and analyses include dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, charts, statistical analyses, genomic signatures, and the ability to generate URLs to live views. We link out to the UCSC Genome Browser as well as MuPIT/CRAVAT and TumorMap. New features include: * Data from PCAWG, latest data from the GDC, ATAC-seq from TCGA, and other studies like MET500 * New visualizations for ATAC-seq and DNA methylation data * Multiple survival endpoints for Kaplan-Meier analyses from the PanCan Atlas * Export PDFs from Chart View * Genomic signatures now supported for all datasets, including data from the GDC * Updated navigation to make it easier to dive into any genomic region * Better support for probes (e.g. methylation probes like "cg16203911") We are now published in Nature Biotechnology! If you use us, cite us here: https://www.nature.com/articles/s41587-020-0546-8 We have also started to visualize scRNA-seq data including data from the HCA and the literature. Our beta prototype site delivers million-cell-scale multi-omics data for interactive visualization in a web browser. Contact us for access to our beta prototype site. Citation Format: Mary J. Goldman, Brian Craft, Jing-chun Zhu, David Haussler. UCSC Xena for the visualization and analysis of cancer genomics data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 250.