Name
Title | ||
|---|---|---|
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. |
Abstract | ||
|---|---|---|
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 userfriendly 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/similar to mybs/. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1093/nar/gkm379 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
transcription factor,computational biology,sequence alignment,position weight matrix,binding site,internet,algorithms,gene regulation,gene targeting,dynamic binding,protein binding,transcription factors,chip,binding sites,chromatin immunoprecipitation,dna chip,transcription factor binding site | Sequence alignment,Promoter,Gene,Biology,DNA binding site,Phylogenetic footprinting,Genetics,Consensus sequence,Molecular biology,Transcription factor,DNA microarray | Journal |
Volume | Issue | ISSN |
35 | SUPnan | 0305-1048 |
Citations | PageRank | References |
11 | 1.21 | 12 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Huai-Kuang Tsai | 1 | 132 | 14.33 |
| Meng-Yuan Chou | 2 | 49 | 3.73 |
| Ching-Hua Shih | 3 | 13 | 1.95 |
| Grace Tzu-Wei Huang | 4 | 20 | 2.39 |
| Tien-Hsien Chang | 5 | 11 | 1.21 |
| Wen-Hsiung Li | 6 | 336 | 24.03 |