title: coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data.
abstract: BACKGROUND
  ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed.
  
  
  RESULTS
  We present a finite mixture framework with an expectation-maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence of Foxa2 with Hnf4a, Cebpa, E-box, Ap1/Maf or Sp1 motifs in ~6-33% of these sequences. These motifs are either known as liver-specific transcription factors or have an important role in liver function.
  
  
  BACKGROUND
  Freely available at http://www.niehs.nih.gov/research/resources/software/comotif/.
  
  
  BACKGROUND
  li3@niehs.nih.gov
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
authors.forename: Mengyuan
authors.initials: M
authors.lastname: Xu
authors.forename: Clarice R
authors.initials: CR
authors.lastname: Weinberg
authors.forename: David M
authors.initials: DM
authors.lastname: Umbach
authors.forename: Leping
authors.initials: L
authors.lastname: Li
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods; D005786:Gene Expression Regulation; D016678:Genome; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D011485:Protein Binding / Q000235:genetics; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors