C2Analyzer

C2Analyzer analyzes co-targeting and co-functional relationships among microRNAs (miRNAs) to identify statistically enriched miRNA pairs and their shared target mRNAs with Gene Ontology (GO) term associations at the post-transcriptional level.

Key Features:

• Hypergeometric Analysis: Uses hypergeometric analysis to test whether pairs of miRNAs are significantly co-functionally enriched based on overlap of target sets.
• Gene Ontology (GO) Term Enrichment: Identifies miRNA sets whose target mRNAs are enriched for specific GO terms to link miRNA targeting to biological processes, molecular functions, or cellular components.
• Co-targeting and Co-functional Relationships: Detects co-targeting miRNA pairs and reports their shared target mRNAs along with associated GO processes.
• Data Export and Visualization: Exports identified miRNA–miRNA co-functional relationships in .txt format for downstream visualization with tools such as Cytoscape.

Scientific Applications:

• Combinatorial miRNA regulation analysis: Enables identification of miRNA pairs that potentially collaborate to regulate common target mRNAs.
• Functional annotation of miRNA targets: Facilitates linking miRNA target sets to GO-defined biological processes and molecular functions.
• Regulatory network construction: Provides co-functional relationships and exportable data to support construction of miRNA-centric regulatory networks.

Methodology:

Implemented as a Perl-based application that applies hypergeometric analysis to assess co-functional enrichment, identifies co-targeting miRNA pairs and their shared target mRNAs with GO mappings, and exports results to .txt for visualization in Cytoscape.