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DNA Research Advance Access originally published online on September 15, 2006
DNA Research 2006 13(3):123-134; doi:10.1093/dnares/dsl005
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome

Alexei A. Sharov, Dawood B. Dudekula and Minoru S. H. Ko*

Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, National Institutes of Health 333 Cassell Drive, Suite 3000, Baltimore, MD 21224, USA

To facilitate the analysis of gene regulatory regions of the mouse genome, we developed a CisView (http://lgsun.grc.nia.nih.gov/cisview), a browser and database of genome-wide potential transcription factor binding sites (TFBSs) that were identified using 134 position-weight matrices and 219 sequence patterns from various sources and were presented with the information about sequence conservation, neighboring genes and their structures, GO annotations, protein domains, DNA repeats and CpG islands. Analysis of the distribution of TFBSs revealed that many TFBSs (N = 145) were over-represented near transcription start sites. We also identified potential cis-regulatory modules (CRMs) defined as clusters of conserved TFBSs in the entire mouse genome. Out of 739 074 CRMs, 157 442 had a significantly higher regulatory potential score than semi-random sequences generated with a 3rd-order Markov process. The CisView browser provides a user-friendly computer environment for studying transcription regulation on a whole-genome scale and can also be used for interpreting microarray experiments and identifying putative targets of transcription factors.

Key words: transcription factor binding site; evolutionary conservation; promoter; enhancer; CpG island; transcription start site

*To whom correspondence should be addressed. Tel. +1-410-558-8359; Fax. +1-410-558-8331, Email: kom{at}mail.nih.gov

Communicated by Kenta Nakai


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