MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.
Correct interactions between transcription factors (TFs) and their binding sites (TFBSs) are of central importance to gene regulation. Recently developed chromatin-immunoprecipitation DNA chip (ChIP-chip) techniques and the phylogenetic footprinting method provide ways to identify TFBSs with high precision. In this study, we constructed a user-friendly interactive platform for dynamic binding site mapping using ChIP-chip data and phylogenetic footprinting as two filters. MYBS (Mining Yeast Binding Sites) is a comprehensive web server that integrates an array of both experimentally verified and predicted position weight matrixes (PWMs) from eleven databases, including 481 binding motif consensus sequences and 71 PWMs that correspond to 183 TFs. MYBS users can search within this platform for motif occurrences (possible binding sites) in the promoters of genes of interest via simple motif or gene queries in conjunction with the above two filters. In addition, MYBS enables users to visualize in parallel the potential regulators for a given set of genes, a feature useful for finding potential regulatory associations between TFs. MYBS also allows users to identify target gene sets of each TF pair, which could be used as a starting point for further explorations of TF combinatorial regulation. MYBS is available at http://cg1.iis.sinica.edu.tw/~mybs/.
Tsai
Huai-Kuang
HK
Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan. hktsai@iis.sinica.edu.tw
Chou
Meng-Yuan
MY
Shih
Ching-Hua
CH
Huang
Grace Tzu-Wei
GT
Chang
Tien-Hsien
TH
Li
Wen-Hsiung
WH
D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018390:Gene Targeting / Q000379:methods*; D020407:Internet; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors