miRsponge

miRsponge identifies and analyzes microRNA (miRNA) sponge interactions and modules to study their regulatory roles, particularly in cancer research such as breast invasive carcinoma (BRCA).

Key Features:

• Identification of miRNA sponge interactions: Incorporates popular computational methods for detecting miRNA sponge interactions from expression and interaction data.
• Integrative analysis: Integrates miRNA sponge interactions derived from different methodologies to provide a consolidated interaction set.
• Validation functions: Provides functions to validate computationally predicted miRNA sponge interactions against experimentally confirmed interactions.
• Inference of miRNA sponge modules (miRSM): Employs the miRSM in silico method to infer miRNA sponge modules with an application focus on breast cancer.
• Enrichment and survival analysis: Conducts enrichment analysis of inferred modules and performs survival analysis to relate modules to patient outcomes.

Scientific Applications:

• Cancer research: Elucidates regulatory networks involving miRNA sponges relevant to oncogenesis and tumor progression.
• Breast cancer module discovery: Identifies functionally significant miRNA sponge modules in breast invasive carcinoma (BRCA), including analyses using TCGA datasets.
• Functional and prognostic assessment: Assesses module-level functional enrichment and associations with patient survival.
• Support for experimental validation: Aids in recovering and corroborating experimentally confirmed miRNA sponge interactions.

Methodology:

Incorporation of multiple computational detection methods and integration of interactions from different methodologies; miRSM in silico method for inference of miRNA sponge modules (applied to breast cancer); enrichment and survival analyses of inferred modules; validation by recovering experimentally confirmed interactions and comparison against benchmark methods.