{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:10:48Z","timestamp":1762521048456},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identifying transcription factor binding sites (TFBSs) is helpful for understanding the mechanism of transcriptional regulation. The abundance and the diversity of genomic data provide an excellent opportunity for identifying TFBSs. Developing methods to integrate various types of data has become a major trend in this pursuit.<\/jats:p>\n               <jats:p>Results: We develop a TFBS identification method, TFBSfinder, which utilizes several data sources, including DNA sequences, phylogenetic information, microarray data and ChIP-chip data. For a TF, TFBSfinder rigorously selects a set of reliable target genes and a set of non-target genes (as a background set) to find overrepresented and conserved motifs in target genes. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0whli@uchicago.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available on Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl160","type":"journal-article","created":{"date-parts":[[2006,4,28]],"date-time":"2006-04-28T00:29:44Z","timestamp":1146184184000},"page":"1675-1681","source":"Crossref","is-referenced-by-count":24,"title":["Method for identifying transcription factor binding sites in yeast"],"prefix":"10.1093","volume":"22","author":[{"given":"Huai-Kuang","family":"Tsai","sequence":"first","affiliation":[{"name":"Genomics Research Center, Academia Sinica 1 \u00a0 1 \u00a0 \u00a0 Taipei, 115 Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grace Tzu-Wei","family":"Huang","sequence":"additional","affiliation":[{"name":"Genomics Research Center, Academia Sinica 1 \u00a0 1 \u00a0 \u00a0 Taipei, 115 Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meng-Yuan","family":"Chou","sequence":"additional","affiliation":[{"name":"Institute of Information Science, Academia Sinica 2 \u00a0 2 \u00a0 \u00a0 Taipei, 115 Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry Horng-Shing","family":"Lu","sequence":"additional","affiliation":[{"name":"Institute of Statistics, National Chiao Tung University 3 \u00a0 3 \u00a0 \u00a0 1001 Ta Hsueh Road, Hsinchu 30050, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Hsiung","family":"Li","sequence":"additional","affiliation":[{"name":"Genomics Research Center, Academia Sinica 1 \u00a0 1 \u00a0 \u00a0 Taipei, 115 Taiwan"},{"name":"Department of Ecology and Evolution, University of Chicago 4 \u00a0 4 \u00a0 \u00a0 1101 East 57th Street, Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,4,27]]},"reference":[{"key":"2023012408542172600_b1","first-page":"21","article-title":"The value of prior knowledge in discovering motifs with MEME","volume":"3","author":"Bailey","year":"1995","journal-title":"Proc. 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