miRSystem

miRSystem integrates multiple miRNA target prediction algorithms and pathway databases to identify miRNA target genes and perform pathway enrichment analysis for characterization of miRNA-regulated biological processes.

Key Features:

• Integration of Multiple Algorithms: Incorporates seven miRNA target gene prediction programs—DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan—and cross-validates predictions across them to enhance reliability.
• Annotation Conversion: Converts queried miRNA IDs to their latest annotated versions to address inconsistencies from frequent miRNA nomenclature updates.
• Consistency-Based Prediction: Evaluates consistency across independent algorithms and applies observed/expected ratio analysis to identify potential gene targets of miRNAs.
• Pathway Enrichment Analysis: Uses five pathway databases and bootstrap approaches to identify significantly enriched pathways associated with predicted target genes.

Scientific Applications:

• Target Prediction and Functional Characterization: Predicts miRNA targets and associated pathways to support interpretation of miRNA-mediated regulation of biological functions and mechanisms.
• Pathway Analysis: Identifies enriched pathways linked to miRNA targets to provide insights into disease mechanisms or potential therapeutic targets.
• Cross-Study Comparisons: Standardizes miRNA nomenclature and integrates multiple prediction algorithms to enable comparative analyses across datasets or research groups.

Methodology:

Converts queried miRNAs to the latest annotated versions.
Integrates predictions from DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan and assesses consistency using observed/expected ratios.
Performs pathway enrichment using five pathway databases with bootstrap methods to identify significant pathways.