Predicting transcription factor binding sites using local over-representation and comparative genomics.

ABSTRACT:

Background

Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs) in coexpressed or coregulated genes. However, this is a challenging problem, especially when considering higher eukaryotic organisms.

Results

We have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position weight matrices. The novelty of the method is that it takes advantage of spatial conservation in the sequence and supports multiple species. The efficiency of the underlying algorithm and its robustness to noise allow weak regulatory

SUBMITTER: Defrance M 

PROVIDER: S-EPMC1570149 | biostudies-literature | 2006 Aug

REPOSITORIES: biostudies-literature