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

doi:10.1093/nar/gks1008

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 journal › Article › peer-review

138 Scopus citations

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 language	English (US)
Pages (from-to)	D949-D954
Journal	Nucleic acids research
Volume	41
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gks1008
State	Published - Jan 1 2013
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gks1008

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title = "The UCSC cancer genomics browser: Update 2013",

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.",

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

note = "Funding Information: National Cancer Institute (NCI) [5U24CA143858]; American Association for Cancer Research (AACR) Stand Up To Cancer (SU2C) program [SU2C-AACR-DT0409]; UCSF Helen Diller Family Comprehensive Cancer Center. Funding for open access charge: Howard Hughes Medical Institute.",

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doi = "10.1093/nar/gks1008",

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AU - Goldman, Mary

AU - Craft, Brian

AU - Swatloski, Teresa

AU - Ellrott, Kyle

AU - Cline, Melissa

AU - Diekhans, Mark

AU - Ma, Singer

AU - Wilks, Chris

AU - Stuart, Josh

AU - Haussler, David

AU - Zhu, Jingchun

N1 - Funding Information: National Cancer Institute (NCI) [5U24CA143858]; American Association for Cancer Research (AACR) Stand Up To Cancer (SU2C) program [SU2C-AACR-DT0409]; UCSF Helen Diller Family Comprehensive Cancer Center. Funding for open access charge: Howard Hughes Medical Institute.

PY - 2013/1/1

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N2 - 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.

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The UCSC cancer genomics browser: Update 2013

Abstract

ASJC Scopus subject areas

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