{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T09:04:47Z","timestamp":1749459887175},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Transcription factor interactions are the cornerstone of combinatorial control, which is a crucial aspect of the gene regulatory system. Understanding and predicting transcription factor interactions based on their sequence alone is difficult since they are often part of families of factors sharing high sequence identity. Given the scarcity of experimental data on interactions compared to available sequence data, however, it would be most useful to have accurate methods for the prediction of such interactions.<\/jats:p>\n               <jats:p>Results: We present a method consisting of a Random Forest-based feature-selection procedure that selects relevant motifs out of a set found using a correlated motif search algorithm. Prediction accuracy for several transcription factor families (bZIP, MADS, homeobox and forkhead) reaches 60\u201390%. In addition, we identified those parts of the sequence that are important for the interaction specificity, and show that these are in agreement with available data. We also used the predictors to perform genome-wide scans for interaction partners and recovered both known and putative new interaction partners.<\/jats:p>\n               <jats:p>Contact: \u00a0roeland.vanham@wur.nl<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm539","type":"journal-article","created":{"date-parts":[[2007,11,18]],"date-time":"2007-11-18T01:26:02Z","timestamp":1195349162000},"page":"26-33","source":"Crossref","is-referenced-by-count":13,"title":["Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control"],"prefix":"10.1093","volume":"24","author":[{"given":"A.D.J.","family":"van Dijk","sequence":"first","affiliation":[{"name":"1 Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 2Biometris, Wageningen UR, Bornsesteeg 47 and 3Bioscience, PRI, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands"}]},{"given":"C.J.F.","family":"ter Braak","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 2Biometris, Wageningen UR, Bornsesteeg 47 and 3Bioscience, PRI, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands"}]},{"given":"R.G.","family":"Immink","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 2Biometris, Wageningen UR, Bornsesteeg 47 and 3Bioscience, PRI, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands"}]},{"given":"G.C.","family":"Angenent","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 2Biometris, Wageningen UR, Bornsesteeg 47 and 3Bioscience, PRI, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands"}]},{"given":"R.C.H.J.","family":"van Ham","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics, PRI, Wageningen UR, Droevendaalsesteeg 1, 2Biometris, Wageningen UR, Bornsesteeg 47 and 3Bioscience, PRI, Wageningen UR, Droevendaalsesteeg 1, Wageningen, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2007,11,17]]},"reference":[{"key":"2023020209444868100_B1","doi-asserted-by":"crossref","first-page":"3026","DOI":"10.1111\/j.1742-4658.2005.04716.x","article-title":"Slc12a2 is a direct target of two closely related homeobox proteins, Six1 and Six4","volume":"272","author":"Ando","year":"2005","journal-title":"FEBS J"},{"key":"2023020209444868100_B2","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.sbi.2004.05.004","article-title":"Structure and evolution of transcriptional regulatory networks","volume":"14","author":"Babu","year":"2004","journal-title":"Curr. 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