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Genome Biol. 2008 Jan 28;9(1):R22. doi: 10.1186/gb-2008-9-1-r22.

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.

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  • 1Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.


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.

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