Name
Title | ||
|---|---|---|
CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. |
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/. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1093/nar/gki486 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
gene expression,binding site,transcription regulation,web interface | Promoter,Conserved sequence,Transcriptional regulation,Phylogenetic tree,Gene,Biology,Genomics,Regulation of gene expression,Genetics,Regulatory sequence | Journal |
Volume | Issue | ISSN |
33 | SUPnan | 0305-1048 |
Citations | PageRank | References |
3 | 0.70 | 0 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Anil G Jegga | 1 | 417 | 24.88 |
| Ashima Gupta | 2 | 93 | 9.17 |
| Sivakumar Gowrisankar | 3 | 35 | 2.36 |
| Mrunal A. Deshmukh | 4 | 5 | 1.09 |
| Steven Connolly | 5 | 3 | 0.70 |
| Kevin Finley | 6 | 3 | 0.70 |
| Bruce J Aronow | 7 | 357 | 19.70 |