title: Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.
abstract: BACKGROUND
  As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations.
  
  
  RESULTS
  We developed a novel method to combine comparative genomics with de novo motif discovery to identify human transcription factor binding motifs that are overrepresented and conserved in the upstream regions of a set of co-regulated genes. The method is validated by analyzing a well-characterized muscle specific gene set, and the results showed that our approach performed better than the existing programs in terms of sensitivity and prediction rate.
  
  
  CONCLUSIONS
  The newly developed method can be used to extract regulatory signals in co-regulated genes, which can be derived from the microarray clustering analysis.
authors.affiliation: Department of Biostatistics, Bioinformatics and Epidemiology, and Bioinformatics Core Facility, Hollings Cancer Center, Medical University of South Carolina, 135 Cannon Street, Charleston, SC 29425, USA. maol@musc.edu
authors.forename: Linyong
authors.initials: L
authors.lastname: Mao
authors.forename: W Jim
authors.initials: WJ
authors.lastname: Zheng
mesh_terms: D020816:Amino Acid Motifs; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors; D004247:DNA