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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Drosophila / genetics*
  • Enhancer Elements, Genetic*
  • Genes, Insect