{"doi":"10.1093/bioinformatics/btr614","title":"Epigenetic priors for identifying active transcription factor binding sites","abstract":"<h4>Motivation</h4>Accurate knowledge of the genome-wide binding of transcription factors in a particular cell type or under a particular condition is necessary for understanding transcriptional regulation. Using epigenetic data such as histone modification and DNase I, accessibility data has been shown to improve motif-based in silico methods for predicting such binding, but this approach has not yet been fully explored.<h4>Results</h4>We describe a probabilistic method for combining one or more tracks of epigenetic data with a standard DNA sequence motif model to improve our ability to identify active transcription factor binding sites (TFBSs). We convert each data type into a position-specific probabilistic prior and combine these priors with a traditional probabilistic motif model to compute a log-posterior odds score. Our experiments, using histone modifications H3K4me1, H3K4me3, H3K9ac and H3K27ac, as well as DNase I sensitivity, show conclusively that the log-posterior odds score consistently outperforms a simple binary filter based on the same data. We also show that our approach performs competitively with a more complex method, CENTIPEDE, and suggest that the relative simplicity of the log-posterior odds scoring method makes it an appealing and very general method for identifying functional TFBSs on the basis of DNA and epigenetic evidence.<h4>Availability and implementation</h4>FIMO, part of the MEME Suite software toolkit, now supports log-posterior odds scoring using position-specific priors for motif search. A web server and source code are available at http://meme.nbcr.net. Utilities for creating priors are at http://research.imb.uq.edu.au/t.bailey/SD/Cuellar2011.<h4>Contact</h4>t.bailey@uq.edu.au<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2011,"id":9509,"datarank":0.7009243251692859,"base_score":4.672828834461906,"endowment":4.672828834461906,"self_citation_contribution":0.7009243251692859,"citation_network_contribution":0.0,"self_endowment_contribution":0.7009243251692859,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":106,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0641,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2011-11-08","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":29558,"name":"Fabian A. Buske","orcid":null,"position":1,"is_corresponding":false},{"id":79780,"name":"Robert C. McLeay","orcid":null,"position":2,"is_corresponding":false},{"id":79781,"name":"Tom Whitington","orcid":null,"position":3,"is_corresponding":false},{"id":4958,"name":"William Stafford Noble","orcid":"0000-0001-7283-4715","position":4,"is_corresponding":false},{"id":29556,"name":"Timothy L. Bailey","orcid":"0000-0002-7018-9342","position":5,"is_corresponding":false},{"id":79779,"name":"Gabriel Cuellar-Partida","orcid":null,"position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}