Computational discovery of <Emphasis Type="Italic">cis</Emphasis>-regulatory modules in <Emphasis Type="Italic">Drosophila</Emphasis> without prior knowledge of motifs |
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| Authors: | Andra Ivan Marc S Halfon Saurabh Sinha |
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| Institution: | (1) Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, N. Goodwin Ave, Urbana, IL 61801, USA;(2) Department of Biochemistry, State University of New York at Buffalo, Main St, Buffalo, NY 14214, USA;(3) New York State Center of Excellence in Bioinformatics and the Life Sciences, Ellicott St, Buffalo, NY 14203, USA |
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| 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. |
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