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.