title: Method for identifying transcription factor binding sites in yeast.
abstract: BACKGROUND
  Identifying transcription factor binding sites (TFBSs) is helpful for understanding the mechanism of transcriptional regulation. The abundance and the diversity of genomic data provide an excellent opportunity for identifying TFBSs. Developing methods to integrate various types of data has become a major trend in this pursuit.
  
  
  RESULTS
  We develop a TFBS identification method, TFBSfinder, which utilizes several data sources, including DNA sequences, phylogenetic information, microarray data and ChIP-chip data. For a TF, TFBSfinder rigorously selects a set of reliable target genes and a set of non-target genes (as a background set) to find overrepresented and conserved motifs in target genes. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods.
  
  
  BACKGROUND
  http://cg1.iis.sinica.edu.tw/~TFBSfinder/.
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan.
authors.forename: Huai-Kuang
authors.initials: HK
authors.lastname: Tsai
authors.forename: Grace Tzu-Wei
authors.initials: GT
authors.lastname: Huang
authors.forename: Meng-Yuan
authors.initials: MY
authors.lastname: Chou
authors.forename: Henry Horng-Shing
authors.initials: HH
authors.lastname: Lu
authors.forename: Wen-Hsiung
authors.initials: WH
authors.lastname: Li
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D018390:Gene Targeting / Q000379:methods*; 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*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors