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DNA Research Advance Access published online on September 15, 2006
DNA Research, doi:10.1093/dnares/dsl005
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© The Author 2006. Kazusa DNA Research Institute.
Received May 8, 2006
Revised July 23, 2006

Full Papers

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

Alexei A. Sharov 1, Dawood B. Dudekula 1, and Minoru S. H. Ko 1 *

1 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 whom correspondence should be addressed.
Minoru S. H. Ko, E-mail: kom{at}mail.nih.gov


  Abstract

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.

Keywords: transcription factor binding site; evolutionary conservation; promoter; enhancer; CpG island; transcription start site.
Communicated by Kenta Nakai
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