ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.

ABSTRACT:

Background

The detection of cis-regulatory modules (CRMs) that mediate transcriptional responses in eukaryotes remains a key challenge in the postgenomic era. A CRM is characterized by a set of co-occurring transcription factor binding sites (TFBS). In silico methods have been developed to search for CRMs by determining the combination of TFBS that are statistically overrepresented in a certain geneset. Most of these methods solve this combinatorial problem by relying on computational intensive optimization methods. As a result their usage is limited to finding CRMs in small datasets (containing a few genes only) and using binding sites for a restricted number of transcription factors (TFs) out of which the optimal module will be selected.

Results

We present an itemset minin

SUBMITTER: Sun H 

PROVIDER: S-EPMC2648767 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature