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G3 (Bethesda). 2012 Sep;2(9):987-1002. doi: 10.1534/g3.112.003202. Epub 2012 Sep 1.

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

Author information

1
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada.

Abstract

oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with known sets of co-regulated genes and published ChIP-Seq data demonstrates the capacity for oPOSSUM-3 to identify mediating transcription factors (TF) for co-regulated genes or co-recovered sequences. oPOSSUM-3 is available at http://opossum.cisreg.ca.

KEYWORDS:

ChIP-Seq; gene regulation; transcription; transcription factor binding sites (TFBS)

PMID:
22973536
PMCID:
PMC3429929
DOI:
10.1534/g3.112.003202
[Indexed for MEDLINE]
Free PMC Article
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