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. 2013 Jan;41(Database issue):D949-54.
doi: 10.1093/nar/gks1008. Epub 2012 Oct 29.

The UCSC Cancer Genomics Browser: update 2013

Mary Goldman  1 , Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa Cline, Mark Diekhans, Singer Ma, Chris Wilks, Josh Stuart, David Haussler, Jingchun Zhu
Affiliations

The UCSC Cancer Genomics Browser: update 2013

Mary Goldman et al. Nucleic Acids Res. 2013 Jan.

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.

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Figures

Figure 1.
Figure 1.
TCGA GBM datasets showing differential copy number variation, gene expression and methylation for the glioma-CpG island methylator phenotype (G-CIMP). The black box emphasizes the samples characterized as G-CIMP tumors. Copy number and DNA methylation datasets, by default, use red and blue to represent amplification and deletion, respectively. Gene expression datasets, by default, use red and green to represent over- and under-expression, respectively. For the G-CIMP clinical feature, yellow represents tumors characterized as G-CIMP and black represents tumors who are not. For the gene expression subtype clinical feature the four subtypes, from black to bright yellow, are proneural, neural, classical, and mesenchymal. (A) TCGA GBM whole genome copy number profile. (B) TCGA GBM gene expression for a select set of genes. (C) TCGA GBM DNA methylation for a select set of genes.
Figure 2.
Figure 2.
Screenshot from user documentation highlighting features in the new user interface.
See this image and copyright information in PMC

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