The UCSC cancer genomics browser: Update 2013

Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa Cline, Mark Diekhans, Singer Ma, Chris Wilks, Josh Stuart, David Haussler, Jingchun Zhu

Research output: Contribution to journalArticle

106 Citations (Scopus)

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.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013
Externally publishedYes

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Genomics
Neoplasms
Genome
Encyclopedias
Atlases
Information Storage and Retrieval
Base Pairing
Documentation
Cell Line

ASJC Scopus subject areas

  • Genetics

Cite this

Goldman, M., Craft, B., Swatloski, T., Ellrott, K., Cline, M., Diekhans, M., ... Zhu, J. (2013). The UCSC cancer genomics browser: Update 2013. Nucleic Acids Research, 41(D1). https://doi.org/10.1093/nar/gks1008

The UCSC cancer genomics browser : Update 2013. / Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; Zhu, Jingchun.

In: Nucleic Acids Research, Vol. 41, No. D1, 01.01.2013.

Research output: Contribution to journalArticle

Goldman, M, Craft, B, Swatloski, T, Ellrott, K, Cline, M, Diekhans, M, Ma, S, Wilks, C, Stuart, J, Haussler, D & Zhu, J 2013, 'The UCSC cancer genomics browser: Update 2013', Nucleic Acids Research, vol. 41, no. D1. https://doi.org/10.1093/nar/gks1008
Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M et al. The UCSC cancer genomics browser: Update 2013. Nucleic Acids Research. 2013 Jan 1;41(D1). https://doi.org/10.1093/nar/gks1008
Goldman, Mary ; Craft, Brian ; Swatloski, Teresa ; Ellrott, Kyle ; Cline, Melissa ; Diekhans, Mark ; Ma, Singer ; Wilks, Chris ; Stuart, Josh ; Haussler, David ; Zhu, Jingchun. / The UCSC cancer genomics browser : Update 2013. In: Nucleic Acids Research. 2013 ; Vol. 41, No. D1.
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