CisView: A browser and database of cis-regulatory modules predicted in the mouse genome

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

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

To facilitate the analysis of gene regulatory regions of the mouse genome, we developed a CisView (http:x//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.

Original languageEnglish
Pages (from-to)123-134
Number of pages12
JournalDNA Research
Volume13
Issue number3
DOIs
Publication statusPublished - 2006
Externally publishedYes

Keywords

  • CpG island
  • Enhancer
  • Evolutionary conservation
  • Promoter
  • Transcription factor binding site
  • Transcription start site

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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