ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
(0) 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 mining based strategy for computationally detecting cisregulatory modules (CRMs) in a set of genes. We tested our method by applying it on a large benchmark data set, derived from a ChiP-Chip analysis and compared its performance with other well known cis-regulatory module detection tools.Conclusions: We show that by exploiting the computational efficiency of an itemset mining approach and combining it with a well designed statistical scoring scheme, we were able to prioritize the biologically valid CRMs in a large set of coregulated genes using binding sites for a large number of potential TFs as input.
Hong Sun Tijl De Bie Valerie Storms Qiang Fu Thomas Dhollander Karen Lemmens Annemieke Verstuyf Bart De Moor Kathleen Marchal
Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpart Arenberg 10, 3001 Department of Engineering Mathematics, university of Bristol, Bristol BS8 1TR, UK Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Kasteelpart Arenberg Laboratory for experimental medicine and endocrinology, Katholieke Universiteit Leuven, 3000 Leuven,
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
347-359
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）