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UCSC Cancer Genomics Browser


NAR Molecular Biology Database Collection entry number 1452
Craft, B., Swatloski, T., Goldman, M., Ellrott, K., Ma, S., Wilks, C., Stuart, J., Haussler, D., and Zhu, J.
Center for Biomolecular Science and Engineering, University of California Santa Cruz, 1156 High St., Santa Cruz, CA, USA

Database Description

The UCSC Cancer Genomics Browser is a web-based tool to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of experimental measurements for multiple samples, alongside their associated clinical information. Multiple datasets can be viewed simultaneously as coordinated “heatmap tracks” to compare across studies or different data modalities, such as gene expression and copy number variation. The browser provides interactive and dynamic views of the data from whole-genome to base-pair scale resolution, as well as zooming into a subset of samples. Users can order, filter, aggregate, classify, and display data interactively based on any given feature set including clinical features, genomic signatures/profiles, annotated biological pathways, and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available datasets.

The browser currently contains a total of 355 datasets, including 201 TCGA public-tier datasets from 22 TCGA cancer projects, data from the cancer cell line encyclopedia project, and 43 other published studies, corresponding to genome-wide experiments from 71870 samples. A controlled access mechanism is also available for private data that currently supports the Stand Up To Cancer breast cancer dream team, ISPY trial, LINCS (Library of Integrated Network-based Cellular Signatures) project and others. In addition, we have a Google-maps-based microscope slide viewer with 2433 slides. The browser is integrated with the UCSC Genome Browser allowing the browser to inherit and integrate with the Genome Browser’s rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.

Recent Developments

In July 2012 a new UCSC Cancer Genomics Browser was released with an updated user interface allowing easy dataset selection as well as grouping of samples for comparison and running statistical analyses. Additionally, users can now download the processed data behind the browser display. Updated documentation and an online interactive tutorial guide users on how to use the browser.

In tandem with the software release, we released updated TCGA data (June 2012) including RNAseqV2, produced by UNC's new version of the data analysis pipeline, and AffyU133 gene expression data. In addition, we released gene expression, copy number, mutation status and response to small molecule inhibitors from the Cancer Cell Line Encyclopedia project. The breast cell line gene expression dataset was updated with recent data published by Laura Heiser et. al. PNAS 2012 109:2724-2729.

Acknowledgements

We would like to thank all the staff at the UCSC Cancer Browser for the data wrangling, curation, release, management and software development. We would also like to thank the UCSC Genome Browser for their continued support. We are funded by NCI/NIH, NHGRI, American Association for Cancer Research (SU2C), UCSF Comprehensive Cancer Center and California Institute for Quantitative Biosciences (QB3).

Subcategory: Cancer gene databases

Go to the abstract in the NAR 2011 Database Issue.
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