UCSC XenaXena

Make your data available to the world

Mary Goldman26 February 2019

Get your data (e.g. from a publication) out to a wider audience for both visualization and download. Set up a Xena Data Hub, load up your data, configure it to be public, and share the URL.

If you are looking to share data on a Xena Hub with a specific group of people. Xena Hubs can be set up on any server or in the cloud. You control who has access to the Xena Hub by controlling who has access to the server on which it is hosted. To make your data publicly available, simply make the server open to the web.

Example: the Treehouse project

figure

An example of a public Xena Hub hosted by an institution is the Treehouse Hub, which is deployed by the Treehouse project. It hosts RNAseq gene expression data of pediatric cancer samples provided by Treehouse's clinical partners and repositories, harmonized with the UCSC RNAseq recompute compendium dataset of TCGA, TARGET and GTEx samples (Morozova 2017, Vivian 2017). This data is used to facilitate interpretation of a pediatric sample in the context of a large pan-cancer cohort, as all samples were processed by the same bioinformatics pipeline. Since the data hub is set up and hosted separately, Treehouse has complete control over the data and data access. They use the UCSC Xena platform to host and update their public data, allowing it to be downloaded and visualized.

Morozova, O., Salama, S. R., Bjork, I., Goldstein, T. C., Mueller, S., et al. Comparative genomic analysis for pediatric cancer patients evaluated in a California Initiative to Advance Precision Medicine Demonstration Project. Journal of Clinical Oncology 35, TPS10578-TPS10578 (2017)

Vivian, J., Rao, A. A., Nothaft, F. A., Ketchum, C., Armstrong, J., et al. Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology 35, 314-316 (2017).

Improve this page