Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.
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.
Mao
Linyong
L
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
Zheng
W Jim
WJ
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*
D014157:Transcription Factors; D004247:DNA