DCGL

DCGL performs differential co-expression and differential regulation analyses to detect differentially co-expressed links and infer transcription factor-mediated regulatory changes from gene expression data.

Key Features:

• Differential Co-expression Analysis (DCEA): Analyzes co-expression relationships among genes across different conditions to detect differentially co-expressed links (DCLs).
• Differential Regulation Analysis (DRA) module: Extends DCEA outputs by integrating transcription factor (TF)-to-target information to translate co-expression changes into regulatory hypotheses.
• DRsort: Identifies differentially regulated genes (DRGs) and differentially regulated links (DRLs) using TF-to-target information.
• DRrank: Ranks and prioritizes transcription factors according to their potential relevance to the phenotype of interest.
• DRplot: Visualizes differentially co-expressed links and TF-to-target interactions within a network context.
• Optimized implementation: Version 2.0 includes code optimizations aimed at improved computational efficiency.
• R package implementation: Distributed as an R package (DCGL v2.0).

Scientific Applications:

• Identification of novel regulators: Detects candidate regulators, including previously undocumented transcription factors, from gene expression datasets.
• Phenotype-relevant regulatory analysis: Prioritizes transcription factors and regulatory links relevant to phenotypes for studies of disease mechanisms, developmental biology, and other contexts where gene regulation is critical.

Methodology:

Analyzes gene expression co-expression patterns to detect DCLs, integrates transcription factor-to-target information to identify DRGs and DRLs via DRsort, prioritizes TFs with DRrank, and produces network visualizations of DCLs and TF-to-target interactions with DRplot.