DiRE

DiRE predicts distant regulatory elements such as enhancers, repressors, and silencers in higher eukaryotic genomes by integrating gene co-expression, comparative genomics, and transcription factor binding site profiles to characterize their locations and regulatory functions.

Key Features:

• Enhancer Identification (EI) method: Uses the Enhancer Identification (EI) method to identify chromosomal locations and functional characteristics of distant regulatory elements.
• Data integration: Integrates gene co-expression data, comparative genomics, and transcription factor binding site (TFBS) profiles for combined analysis.
• TFBS-association signatures: Analyzes TFBS-association signatures derived from integrated datasets to discern regulatory functions of genomic regions.
• Locus-wide analysis: Detects regulatory elements outside proximal promoter regions by utilizing information across the entire gene locus.
• TFBS cluster identification: Identifies clusters of specifically-associated TFBSs linked to the input gene set.
• Transcription factor association scoring: Scores individual transcription factors' associations with shared biological functions among input gene groups.
• Input flexibility: Accepts any set of genes with prior co-expression or biologically meaningful grouping to predict common distant regulatory elements.
• Array2BIO integration: Integrates with Array2BIO to enable analyses starting from raw microarray expression data.

Scientific Applications:

• Distant regulatory element discovery: Identification and characterization of enhancers, repressors, and silencers in higher eukaryotic genomes.
• Regulatory function annotation: Assigning putative regulatory functions to genomic regions across entire gene loci.
• Transcription factor–function association: Linking transcription factors to shared biological functions in co-expressed or functionally grouped genes.
• Regulatory network analysis: Mapping clusters of TFBSs and TF associations to inform transcriptional regulatory network studies.

Methodology:

Applies the Enhancer Identification (EI) method and integrates gene co-expression data, comparative genomics, and TFBS profiles to derive TFBS-association signatures, identify TFBS clusters, and score TF associations across entire gene loci.