{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:39:39Z","timestamp":1759207179601},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: To understand transcription regulatory mechanisms, it is indispensable to investigate transcription factor (TF) DNA binding preferences. We noted that the generally acknowledged information of functional annotations of TFs as well as that of their target genes should provide useful hints in determining TF DNA binding preferences.<\/jats:p><jats:p>Results: In this contribution, we developed an integrative method based on the Nearest Neighbor Algorithm, to predict DNA binding preferences through integrating both the functional\/structural information of TFs and the interaction between TFs and their targets. The accuracy of cross-validation tests on the dataset consisting of 3430 positive samples and 7000 negative samples reaches 87.0 % for 10-fold cross-validation and 87.9 % for jackknife cross-validation test, which is a much better result than that in our previous work. The prediction result indicates that the improved method we developed could be a powerful approach to infer the TF DNA preference in silico.<\/jats:p><jats:p>Contact: \u00a0cyd@picb.ac.cn<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm348","type":"journal-article","created":{"date-parts":[[2007,7,11]],"date-time":"2007-07-11T01:44:07Z","timestamp":1184118247000},"page":"2449-2454","source":"Crossref","is-referenced-by-count":17,"title":["An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization"],"prefix":"10.1093","volume":"23","author":[{"given":"Ziliang","family":"Qian","sequence":"first","affiliation":[{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"},{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingyi","family":"Lu","sequence":"additional","affiliation":[{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"},{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"XiaoJun","family":"Liu","sequence":"additional","affiliation":[{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Dong","family":"Cai","sequence":"additional","affiliation":[{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"},{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"},{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"},{"name":"2 \u00a01CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, 3Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 4Department of Mathematics, University of Manchester, Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD, UK, 5Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, 200235 Shanghai, 6College of Life Science & Biotechnology, Shanghai Jiao Tong University, China and 7Molecular Physiology Laboratory, Centre for Cardiovascular Science Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,7,10]]},"reference":[{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/29.1.37","article-title":"The InterPro database, an integrated documentation resource for protein families, domains and functional sites","volume":"29","author":"Apweiler","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1093\/bib\/3.3.252","article-title":"The PRINTS database: a resource for identification of protein families","volume":"3","author":"Attwood","year":"2002","journal-title":"Brief. bioinformatics"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"4302","DOI":"10.1016\/j.febslet.2005.07.002","article-title":"Prediction of methylated CpGs in DNA sequence using a support vector machine","volume":"579","author":"Bhasin","year":"2005","journal-title":"FEBS Lett"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.jtbi.2005.05.035","article-title":"Predicting membrane protein type by functional domain composition and pseudo-amino acid composition","volume":"238","author":"Cai","year":"2006","journal-title":"J. Theor. Boil"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/j.bbrc.2004.10.058","article-title":"Using GO-PseAA predictor to predict enzyme sub-class","volume":"325","author":"Chou","year":"2004","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1021\/pr050331g","article-title":"Predicting protein-protein interactions from sequences in a hybridization space","volume":"5","author":"Chou","year":"2006","journal-title":"J. proteome Res"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nbt0806-959","article-title":"How does DNA sequence motif discovery work?","volume":"24","author":"D'Haeseleer","year":"2006","journal-title":"Nat. Biotechnol"},{"key":"2023041106220350700_","first-page":"D247","article-title":"Pfam: clans, web tools and services","author":"Finn","year":"2006"},{"key":"2023041106220350700_","first-page":"1","article-title":"DNase I footprinting","volume":"90","author":"Fox","year":"1997","journal-title":"Methods mol. Biol. (Clifton, N.J.)"},{"key":"2023041106220350700_","first-page":"361","article-title":"Drug discovery with engineered zinc-finger proteins","volume":"2","author":"Jamieson","year":"2003","journal-title":"Nat. rev"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1186\/1471-2105-7-271","article-title":"Demonstration of two novel methods for predicting functional siRNA efficiency","volume":"7","author":"Jia","year":"2006","journal-title":"BMC bioinformatics"},{"key":"2023041106220350700_","volume-title":"Making Large-Scale SVM Learning Practical.","author":"Joachims","year":"1999"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"D108","DOI":"10.1093\/nar\/gkj143","article-title":"TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes","volume":"34","author":"Matys","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.bbrc.2006.06.060","article-title":"Automatic transcription factor classifier based on functional domain composition","volume":"347","author":"Qian","year":"2006","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1016\/j.bbrc.2006.07.149","article-title":"A novel computational method to predict transcription factor DNA binding preferences","volume":"348","author":"Qian","year":"2006","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023041106220350700_","first-page":"16","article-title":"DNA binding sites: representation and discovery","volume":"16","author":"Stormo","year":"2000","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1093\/nar\/24.1.238","article-title":"TRANSFAC: a database on transcription factors and their DNA binding sites","volume":"24","author":"Wingender","year":"1996","journal-title":"Nucleic Acids Res"},{"key":"2023041106220350700_","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/1471-2105-7-187","article-title":"Classification of protein quaternary structure by functional domain composition","volume":"7","author":"Yu","year":"2006","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/18\/2449\/49816824\/bioinformatics_23_18_2449.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/18\/2449\/49816824\/bioinformatics_23_18_2449.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,16]],"date-time":"2024-02-16T14:55:20Z","timestamp":1708095320000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/18\/2449\/236497"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,7,10]]},"references-count":18,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2007,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm348","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,9,15]]},"published":{"date-parts":[[2007,7,10]]}}}