BCC2020

→ Abstract


The presenter(s) will be available for live Q&A in this session (BCC West).

Nathan Dunn 1, Brian Craft 2, Mary Goldman 2, Jing Zhu 2

1 Lawrence Berkeley National Lab, Berkeley, CA. Email: nathandunn@lbl.gov
2 University of California Santa Cruz, Santa Cruz, CA

Live Demo: https://xenageneset.berkeleybop.io/xena/
Source Code: https://github.com/ucscXena/XenaGoWidget
Project Website: https://xena.ucsc.edu/welcome-to-ucsc-xena/
License: (BSD-3-clause https://github.com/ucscXena/XenaGoWidget/blob/develop/LICENSE)

The UCSC Xena platform focuses on the visualization of cancer genomics data
[https://doi.org/10.1101/326470] by providing users with a view of large public cancer genomics
datasets such as TCGA and supports most types of functional genomics data. It uses the Xena Visual
spreadsheet to let users interact with the data by providing powerful filtering, subgrouping, and statistical
analyses. However, the spreadsheet performs analysis only on a per-gene basis, making it difficult to
visually compare sets of genes or pathways at once.
Here, we introduce the Xena GeneSet Viewer, which enables comparison of gene sets between cohorts, or
across varying sample sets from within the same cohort. The Xena GeneSet Viewer can compare activity
of gene expression, copy number variants, and somatic mutation across most of the The Cancer Genome
Atlas (TCGA) public data set.