title: Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.
abstract: We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal.
authors.affiliation: Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Andra
authors.initials: A
authors.lastname: Ivan
authors.forename: Marc S
authors.initials: MS
authors.lastname: Halfon
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004330:Drosophila / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D017344:Genes, Insect