Xena

UCSC Xena

UCSC Xena is a bioinformatics tool to visualize functional genomics data from multiple sources simultaneously, including both public and private data. The Xena system consists of a set of federated data hubs and the Xena browser, which integrates across hubs, providing one location to analyze and visualize all data. The lightweight Xena data hubs are straightforward to install on Windows, Mac and Linux operating systems and easily allow hub administrators to authenticate users, ensuring that only authorized users have access to secure data. Loading data into a Xena hub is easy using either our application or command line interface. We host public data from major projects, such as TCGA, on public Xena hubs, giving users access without having to download these large datasets. While you can view data from each hub separately, the Xena system makes it easy to aggregate any arbitrary number of samples across many hubs, integrating public and/or private data into a ‘virtual cohort’. This allows researchers to combine new or preliminary results from their laptops or internal servers, or even data from a new paper, securely with vetted data from the public sphere.

Our public hubs host 806 public datasets from several large consortiums including TCGA (The Cancer Genome Atlas), ICGC (International Cancer Genome Consortium),Treehouse Childhood Cancer Project, CCLE (Cancer Cell Line Encyclopedia), and more. Xena hubs are flexible enough to handle most data types, including gene, exon, miRNA and protein expression, copy number, DNA methylation, somatic mutation, fusion and structural variant data along with phenotypes, subtype classifications and genomic biomarkers. All our data can be downloaded as slices or in large batches. Our browser instantaneously displays thousands of samples in many different visualization modes, including virtual spreadsheets, scatter plots and bar graphs. Dynamic Kaplan-Meier survival analysis helps investigators to assess survival stratification. Filter, sort, highlight and zoom to any samples of interest.