title: Comparative genomic analysis of transcription regulation elements involved in human map kinase G-protein coupling pathway.
abstract: The identification of cis-elements (motifs) in the regulatory regions of higher eukaryotes is an important and challenging problem in computational biology. Eukaryotic transcriptional regulatory mechanisms pose several difficulties for promoter analysis: including a high variance in the motif locations, frequently large divergence from motif consensus patterns, and a large amount of repetitive elements (confusing to many motif finding procedures). One promising approach to this difficult problem involves cross-species comparison. In this work we analyzed the full-length regulatory regions of genes involved in the G-protein coupling MAP kinase pathway and compared the results with ribosomal genes using human, mouse and rat genomic data. We found 19 high likely transcription factors (TFs) candidates for MAPK and 12 TFs for the ribosomal dataset. In the case of the MAPK dataset, regulatory regions of genes functionally grouped as receptors and MAP-core genes were found mostly highly conserved across the three species.
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-42, Tokyo, 153 - 0061, Japan. nata.polouliakh@aist.go.jp
authors.forename: Natalia
authors.initials: N
authors.lastname: Polouliakh
authors.forename: Tohru
authors.initials: T
authors.lastname: Natsume
authors.forename: Hajime
authors.initials: H
authors.lastname: Harada
authors.forename: Wataru
authors.initials: W
authors.lastname: Fujibuchi
authors.forename: Paul
authors.initials: P
authors.lastname: Horton
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D019204:GTP-Binding Proteins / Q000235:genetics*; D015971:Gene Expression Regulation, Enzymologic / Q000502:physiology*; D006801:Humans; D020935:MAP Kinase Signaling System / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D051381:Rats; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D019204:GTP-Binding Proteins