SpidermiR

SpidermiR integrates microRNA (miRNA) data into gene regulatory networks (GRNs) to enable analysis and visualization of miRNA-mediated regulatory mechanisms.

Key Features:

• Implementation: Provided as an R/Bioconductor package for programmatic analysis.
• Data access and retrieval: Supports querying and downloading GRN and miRNA data from validated and predicted repositories.
• Integration with differentially expressed genes: Integrates miRNA data with GRNs alongside differentially expressed genes from The Cancer Genome Atlas (TCGA).
• Network analysis capabilities: Identifies interactions such as miRNA–gene–gene and miRNA–protein–protein connections and detects miRNA–gene communities.
• Visualization: Generates graphical visualizations of network structures and miRNA–GRN interactions.

Scientific Applications:

• Gene regulatory network analysis: Facilitates exploration of GRN topology and regulatory interactions involving miRNAs.
• miRNA function and interaction studies: Enables identification of miRNA targets, miRNA–gene communities, and indirect regulatory effects.
• Cancer genomics: Supports integration of TCGA differential expression data to study miRNA-mediated regulation in cancer.

Methodology:

Integrates data from validated and predicted miRNA repositories with GRNs derived from The Cancer Genome Atlas (TCGA) and processes full datasets locally to analyze direct and indirect interactions within biological networks.