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coMOTIF: A Mixture Framework for Identifying Transcription Factor and a Co-regulator Motif in ChIP-seq Data.
Bioinformatics. 2011 Jul 19;
Authors: Xu M, Weinberg CR, Umbach DM, Li L
MOTIVATION: ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a co-regulator. Biologists are interested in knowing which co-regulatory 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 ten 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 liver-specific transcription factors or have an important role in liver function. AVAILABILITY: Freely available at http://www.niehs.nih.gov/research/re...tware/comotif/. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID: 21775309 [PubMed - as supplied by publisher]
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coMOTIF: A Mixture Framework for Identifying Transcription Factor and a Co-regulator Motif in ChIP-seq Data.
Bioinformatics. 2011 Jul 19;
Authors: Xu M, Weinberg CR, Umbach DM, Li L
MOTIVATION: ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a co-regulator. Biologists are interested in knowing which co-regulatory 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 ten 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 liver-specific transcription factors or have an important role in liver function. AVAILABILITY: Freely available at http://www.niehs.nih.gov/research/re...tware/comotif/. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID: 21775309 [PubMed - as supplied by publisher]
More...