- The UCSC Cancer Genomics Browser: update 2015. [PMID: 25392408]
Mary Goldman, Brian Craft, Teresa Swatloski, Melissa Cline, Olena Morozova, Mark Diekhans, David Haussler, Jingchun Zhu
Nucleic acids research 2015:43(Database issue)
Citation (to be updated)
Abstract: The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users can explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside clinical and phenotypic features, such as age, subtype classifications and genomic biomarkers. The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227,000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET. Users can download and upload clinical data, generate Kaplan-Meier plots dynamically, export data directly to Galaxy for analysis, plus generate URL bookmarks of specific views of the data to share with others. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- The UCSC Cancer Genomics Browser: update 2013. [PMID: 23109555]
Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa Cline, Mark Diekhans, Singer Ma, Chris Wilks, Josh Stuart, David Haussler, Jingchun Zhu
Nucleic acids research 2013:41(Database issue)
73 Citations (Google Scholar as of 2016-03-02)
Abstract: The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information. The browser provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms. The ability to view multiple datasets together allows users to make comparisons across different data and cancer types. Biological pathways, collections of genes, genomic or clinical information can be used to sort, aggregate and zoom into a group of samples. We currently display an expanding set of data from various sources, including 201 datasets from 22 TCGA (The Cancer Genome Atlas) cancers as well as data from Cancer Cell Line Encyclopedia and Stand Up To Cancer. New features include a completely redesigned user interface with an interactive tutorial and updated documentation. We have also added data downloads, additional clinical heatmap features, and an updated Tumor Image Browser based on Google Maps. New security features allow authenticated users access to private datasets hosted by several different consortia through the public website.
- The UCSC Cancer Genomics Browser: update 2011. [PMID: 21059681]
J Zachary Sanborn, Stephen C Benz, Brian Craft, Christopher Szeto, Kord M Kober, Laurence Meyer, Charles J Vaske, Mary Goldman, Kayla E Smith, Robert M Kuhn, Donna Karolchik, W James Kent, Joshua M Stuart, David Haussler, Jingchun Zhu
Nucleic acids research 2011:39(Database issue)
44 Citations (Google Scholar as of 2016-03-02)
Abstract: The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) 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.
- The UCSC Cancer Genomics Browser. [PMID: 19333237]
Jingchun Zhu, J Zachary Sanborn, Stephen Benz, Christopher Szeto, Fan Hsu, Robert M Kuhn, Donna Karolchik, John Archie, Marc E Lenburg, Laura J Esserman, W James Kent, David Haussler, Ting Wang
Nature methods 2009:6(4)
70 Citations (Google Scholar as of 2016-03-02)