CHRONOS

CHRONOS analyzes time-series mRNA and microRNA expression data to identify microRNA-mediated subpathways and dynamic, condition-specific pathway activity by integrating experimental data with KEGG pathway maps.

Key Features:

• Integration with KEGG Pathway Maps: Integrates time-series mRNA/microRNA expression data with KEGG pathway maps to align experimental signals with curated biological processes.
• MicroRNA-Mediated Subpathway Extraction: Extracts and evaluates microRNA-mediated subpathways by analyzing temporal transitions and fold-change activities of linked genes and microRNAs.
• Dynamic Theme Identification: Identifies multiple dynamic 'themes' of enriched, biologically relevant microRNA-mediated subpathways that vary across temporal conditions.
• Structural and Functional Measures: Computes measures capturing both structural and functional features of subpathways relative to the complete organism pathway atlas.

Scientific Applications:

• Network medicine: Dissects time- and condition-specific active components of biological circuitry from paired time-series mRNA/microRNA experiments.
• MicroRNA signaling analysis: Elucidates how microRNAs influence signaling networks over time to inform interpretation of disease mechanisms and identification of potential therapeutic targets.

Methodology:

Integrates experimental time-series mRNA/microRNA data with KEGG pathway maps and analyzes gene–microRNA interactions, temporal transitions, and fold changes to identify dynamically active subpathways.