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Bioinformatics. 2014 Feb 15;30(4):590-2. doi: 10.1093/bioinformatics/btt710. Epub 2013 Dec 6.

ChromoHub V2: cancer genomics.

Author information

1
Structural Genomics Consortium, and Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5G 1L7, Canada.

Abstract

SUMMARY:

Cancer genomics data produced by next-generation sequencing support the notion that epigenetic mechanisms play a central role in cancer. We have previously developed Chromohub, an open access online interface where users can map chemical, structural and biological data from public repositories on phylogenetic trees of protein families involved in chromatin mediated-signaling. Here, we describe a cancer genomics interface that was recently added to Chromohub; the frequency of mutation, amplification and change in expression of chromatin factors across large cohorts of cancer patients is regularly extracted from The Cancer Genome Atlas and the International Cancer Genome Consortium and can now be mapped on phylogenetic trees of epigenetic protein families. Explorators of chromatin signaling can now easily navigate the cancer genomics landscape of writers, readers and erasers of histone marks, chromatin remodeling complexes, histones and their chaperones.

AVAILABILITY AND IMPLEMENTATION:

http://www.thesgc.org/chromohub/.

PMID:
24319001
PMCID:
PMC3928521
DOI:
10.1093/bioinformatics/btt710
[Indexed for MEDLINE]
Free PMC Article
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