Work

CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes

Year: 2005

Type: article

Abstract: Combinatorial interactions of sequence-specific trans -acting factors with localized genomic cis -element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis -elements responsible for specific patterns of transcriptional regulation represents a critical area of investigation. Computational methods for the identification of functional cis -regulatory modules are difficult to devise, principally because of the short length and degenerate nature of individual cis -element binding sites and the inherent complexity that is generated by combinatorial interactions within cis -clusters. Filtering candidate cis -element clusters based on phylogenetic conservation is helpful for an individual ortholog gene pair, but combining data from cis -conservation and coordinate expression across multiple genes is a more difficult problem. To approach this, we have extended an ortholog gene-pair database with additional analytical architecture to allow for the analysis and identification of maximal numbers of compositionally similar and phylogenetically conserved cis -regulatory element clusters from a list of user-selected genes. The system has been successfully tested with a series of functionally related and microarray profile-based co-expressed ortholog pairs of promoters and genes using known regulatory regions as training sets and co-expressed genes in the olfactory and immunohematologic systems as test sets. CisMols Analyzer is accessible via a Web interface at http://cismols.cchmc.org/ .

Source: Nucleic Acids Research

DOI: 10.1093/nar/gki486