CisMols

CisMols identifies compositionally predicted, evolutionarily conserved cis-regulatory modules within ortholog-pair cis-regulatory regions to detect combinatorial cis-element clusters that regulate tissue-specific and developmental gene expression.

Key Features:

• Identification of Cis-Regulatory Modules: Detects compositionally predicted cis-clusters within ortholog-pair conserved cis-regulatory regions, accounting for short and degenerate cis-element binding sites and combinatorial interactions of sequence-specific trans-acting factors.
• Phylogenetic Conservation Filtering: Leverages phylogenetic conservation across ortholog gene pairs to filter candidate cis-element clusters and prioritize conserved regulatory regions.
• Ortholog Gene-Pair Analytical Architecture: Extends an ortholog gene-pair database with analytical modules to identify compositionally similar and phylogenetically conserved cis-regulatory element clusters from a selected list of genes.

Scientific Applications:

• Gene Expression Regulation: Facilitates analysis of regulatory mechanisms underlying tissue-specific and developmental gene expression via identification of cis-regulatory modules.
• Functional Genomics Studies: Supports studies of co-expressed ortholog pairs of promoters and genes for functional genomics analyses.
• Olfactory and Immunohematologic Systems Research: Has been tested using known regulatory regions as training sets and co-expressed genes in the olfactory and immunohematologic systems as test sets.

Methodology:

Identifies compositionally predicted cis-clusters within ortholog-pair conserved cis-regulatory regions; leverages phylogenetic conservation as a filter; integrates phylogenetic conservation data with coordinate expression across multiple genes; extends an ortholog gene-pair database to analyze compositionally similar, phylogenetically conserved cis-regulatory element clusters; uses known regulatory regions as training sets and co-expressed genes as test sets.