UCSC Cancer Genomics Browser

Other names: ucsc_cancer_genomics_browser

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 tracksâ€\x9D 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.

Webpage:
https://xena.ucsc.edu/welcome-to-ucsc-xena/

Publications:

Tags:

human genes and diseases cancer-related genes oncology molecular interactions, pathways and networks imaging genomics

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