CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes.
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/.
Jegga
Anil G
AG
Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC, 3333 Burnet Avenue, Cincinnati, OH-45229, USA.
Gupta
Ashima
A
Gowrisankar
Sivakumar
S
Deshmukh
Mrunal A
MA
Connolly
Steven
S
Finley
Kevin
K
Aronow
Bruce J
BJ
D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D020407:Internet; D020218:Response Elements; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
D014157:Transcription Factors