The UCSC cancer genomics browser: update 2011

TitleThe UCSC cancer genomics browser: update 2011
Publication TypeJournal Article
Year of Publication2011
AuthorsSanborn, ZJ, Benz, SC, Craft, B, Szeto, C, Kober, KM, Meyer, L, Vaske, CJ, Goldman, M, Smith, KE, Kuhn, RM, Karolchik, D, Kent, JW, Stuart, JM, Haussler, D, Zhu, J
JournalNucleic Acids Research
AbstractThe UCSC Cancer Genomics Browser ( comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated ‘heatmap tracks’ to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and ‘PARADIGM’ pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser’s rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.
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