Identification of over-represented TFBSs in each gene cluster. Upstream genomic sequence (3 kb) was searched for TFBS in evolutionarily conserved regions (ECR) that are over-represented in a gene cluster. Proximal promoter regions (1.2 kb) were searched for over-represented TFBS in the cluster. We also determined the over-represented TFBS frequency in the proximal promoter region for each gene in the cluster. The relative importance of a TFBS was determined by the average ranking order of ECR, prompter and frequency analysis and normalized to -2.5 to 2.5. A heatmap was generated based on the normalized relative importance of TFBSs. ND: Frequency was not determined if the TFBS was not enriched in the promoter region of the gene cluster compared to all promoters in the mouse genome used as the background set (p-value > 0.05).
Xu et al. BMC Genomics 2010 11:451 doi:10.1186/1471-2164-11-451