ASDmiR

ASDmiR infers miRNA-mediated regulatory networks and modules in autism spectrum disorder by integrating miRNA, long non-coding RNA (lncRNA), and mRNA expression data to characterize post-transcriptional regulation.

Key Features:

• Identification of miRNA-target networks: Compares 12 miRNA-target prediction methods using matched miRNA, lncRNA, and mRNA expression data from ASD samples and selects the method that predicts the largest number of experimentally confirmed interactions.
• Inference of regulatory bicliques/modules: Detects regulatory bicliques or modules from the inferred miRNA-target interaction network to reveal functional organization.
• Integration with gene expression data: Integrates high-confidence miRNA-target interactions with expression data to construct lncRNA-lncRNA, lncRNA-mRNA, and mRNA-mRNA miRNA sponge interaction networks.
• Identification of miRNA sponge modules: Infers modules from the miRNA sponge interaction network to identify communities of competing endogenous RNAs.
• Functional enrichment analysis: Performs enrichment analysis on hub genes and network/module components to assess links with ASD pathogenesis.

Scientific Applications:

• Regulatory network characterization: Dissects miRNA-mediated regulatory mechanisms implicated in ASD using integrated expression and interaction data.
• Biomarker and target discovery: Prioritizes hub genes, modules, and miRNA sponges as candidate biomarkers or therapeutic targets for ASD research.
• Systems biology analyses: Enables construction of multi-layered lncRNA–mRNA interaction networks for holistic studies of gene regulation in neurodevelopmental disorders.

Methodology:

Performs a stepwise comparative analysis of 12 miRNA-target prediction methods using matched miRNA, lncRNA, and mRNA expression profiles from ASD samples, selects the best-performing method based on the number of experimentally confirmed interactions predicted, infers regulatory bicliques/modules, integrates high-confidence interactions with expression data to build lncRNA-lncRNA, lncRNA-mRNA, and mRNA-mRNA miRNA sponge networks, infers modules from the sponge network, and conducts functional enrichment analysis of hub genes and modules.