Journal Article

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

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

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 13, issue 3, pages 123-134
Published in print September 2006 | ISSN: 1340-2838
Published online January 2006 | e-ISSN: 1756-1663 | DOI:

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To facilitate the analysis of gene regulatory regions of the mouse genome, we developed a 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

Journal Article.  6977 words.  Illustrated.

Subjects: Genetics and Genomics

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