{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T01:35:10Z","timestamp":1722821710370},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene regulation involves complicated mechanisms such as cooperativity between a set of transcription factors (TFs). Previous studies have used target genes shared by two TFs as a clue to infer TF\u2013TF interactions. However, this task remains challenging because the target genes with low binding affinity are frequently omitted by experimental data, especially when a single strict threshold is employed. This article aims at improving the accuracy of inferring TF\u2013TF interactions by incorporating motif discovery as a fundamental step when detecting overlapping targets of TFs based on ChIP-chip data.<\/jats:p>\n               <jats:p>Results: The proposed method, simTFBS, outperforms three na\u00efve methods that adopt fixed thresholds when inferring TF\u2013TF interactions based on ChIP-chip data. In addition, simTFBS is compared with two advanced methods and demonstrates its advantages in predicting TF\u2013TF interactions. By comparing simTFBS with predictions based on the set of available annotated yeast TF binding motifs, we demonstrate that the good performance of simTFBS is indeed coming from the additional motifs found by the proposed procedures.<\/jats:p>\n               <jats:p>Contact: \u00a0hktsai@iis.sinica.edu.tw; chienyuchen@ntu.edu.tw<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts002","type":"journal-article","created":{"date-parts":[[2012,1,12]],"date-time":"2012-01-12T03:10:30Z","timestamp":1326337830000},"page":"701-708","source":"Crossref","is-referenced-by-count":15,"title":["<i>De novo<\/i> motif discovery facilitates identification of interactions between transcription factors in <i>Saccharomyces cerevisiae<\/i>"],"prefix":"10.1093","volume":"28","author":[{"given":"Mei-Ju May","family":"Chen","sequence":"first","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lih-Ching","family":"Chou","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tsung-Ting","family":"Hsieh","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ding-Dar","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai-Wei","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi-Yuan","family":"Yu","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yen-Jen","family":"Oyang","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of 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Academia Sinica, Taipei, Taiwan"},{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huai-Kuang","family":"Tsai","sequence":"additional","affiliation":[{"name":"1 Genome and Systems Biology Degree Program, 2Department of Computer Science and Information Engineering, 3Department of Bio-Industrial Mechatronics Engineering, 4Graduate Institute of Biomedical Electronics and Bioinformatics, 5Center for Systems Biology, National Taiwan University and 6Institute of Information Science, Academia Sinica, Taipei, 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