title: CoopTFD: a repository for predicted yeast cooperative transcription factor pairs.
abstract: In eukaryotic cells, transcriptional regulation of gene expression is usually accomplished by cooperative Transcription Factors (TFs). Therefore, knowing cooperative TFs is helpful for uncovering the mechanisms of transcriptional regulation. In yeast, many cooperative TF pairs have been predicted by various algorithms in the literature. However, until now, there is still no database which collects the predicted yeast cooperative TFs from existing algorithms. This prompts us to construct Cooperative Transcription Factors Database (CoopTFD), which has a comprehensive collection of 2622 predicted cooperative TF pairs (PCTFPs) in yeast from 17 existing algorithms. For each PCTFP, our database also provides five types of validation information: (i) the algorithms which predict this PCTFP, (ii) the publications which experimentally show that this PCTFP has physical or genetic interactions, (iii) the publications which experimentally study the biological roles of both TFs of this PCTFP, (iv) the common Gene Ontology (GO) terms of this PCTFP and (v) the common target genes of this PCTFP. Based on the provided validation information, users can judge the biological plausibility of a PCTFP of interest. We believe that CoopTFD will be a valuable resource for yeast biologists to study the combinatorial regulation of gene expression controlled by cooperative TFs.Database URL: http://cosbi.ee.ncku.edu.tw/CoopTFD/ or http://cosbi2.ee.ncku.edu.tw/CoopTFD/.
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan wessonwu@mail.ncku.edu.tw.
authors.forename: Wei-Sheng
authors.initials: WS
authors.lastname: Wu
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
authors.forename: Fu-Jou
authors.initials: FJ
authors.lastname: Lai
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
authors.forename: Bor-Wen
authors.initials: BW
authors.lastname: Tu
authors.affiliation: Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
authors.forename: Darby Tien-Hao
authors.initials: DT
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors