Promoter Module Detection as a Tool for Gene Identifcation in Colon Carcinoma

Background: Promoter modules, consisting of at least two transcription factor binding sites at defined distances along a gene, are an integral part of the regulation of gene expression. These modules can be responsible for the control of genes sharing common functions i.e. proliferation

Aims: We hypothesised that genes implicated in the neoplastic process in the colon may share common promoter modules. We used bioinformatic techniques to identify these modules and detect co-regulated genes.

Methods: We used a previously identified list of colon cancer-associated genes as template. We used the software MatInspector to detect individual transcription factor binding sites. Those sites that were experimentally validated were used to detect functional modules using FrameWorker software. Nucleotide sequence databases were then searched for genes containing these modules using ModelInspector

Results: An initial database of 40 genes associated with colon cancer was scanned for transcription factor binding sites. From these 23 promoters were identified in 15 genes. Although a number of individual transcription factor binding sites were prevalent, two common promoter modules were detected in over 80% of genes. Similarly-regulated genes were identified using these modules.

Conclusion: This approach can be used to identify promoter modules implicated in colonic carcinogenesis.