title: 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 mining based strategy for computationally detecting cis-regulatory 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.
authors.affiliation: Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium. hong.sun@esat.kuleuven.be
authors.forename: Hong
authors.initials: H
authors.lastname: Sun
authors.forename: Tijl
authors.initials: T
authors.lastname: De Bie
authors.forename: Valerie
authors.initials: V
authors.lastname: Storms
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fu
authors.forename: Thomas
authors.initials: T
authors.lastname: Dhollander
authors.forename: Karen
authors.initials: K
authors.lastname: Lemmens
authors.forename: Annemieke
authors.initials: A
authors.lastname: Verstuyf
authors.forename: Bart
authors.initials: B
authors.lastname: De Moor
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D030541:Databases, Genetic; D008957:Models, Genetic; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors