MIREyA

MIREyA predicts miRNA–enhancer–gene regulatory trios from expression datasets to identify miRNAs that activate gene expression through enhancer interactions.

Key Features:

• miRNA-Enhancer-Gene Trios Prediction: Predicts triads consisting of miRNAs, target genes, and enhancers by analyzing expression datasets.
• Pipeline Design: Implements a structured pipeline for standardized analysis of expression datasets to identify regulatory relationships among miRNAs, enhancers, and genes.
• Application in Disease Contexts: Applied to primary murine macrophages infected with Mycobacterium tuberculosis (HN878) to identify miRNAs involved in immune response regulation.
• Specific miRNA Identification: Identifies specific miRNAs such as Mir22, Mir221, Mir222, Mir155, and Mir1956 that up-regulate genes associated with immune responses.

Scientific Applications:

• miRNA-mediated gene activation studies: Enables investigation of miRNA roles in activating gene expression via enhancers rather than canonical repression.
• Immune response and host–pathogen interaction analysis: Supports analysis of miRNAs regulating immune responses in contexts such as Mycobacterium tuberculosis infection.
• Genomics, molecular biology, and systems biology: Facilitates identification of regulatory networks involving miRNAs, enhancers, and genes in genomic and systems-level studies.

Methodology:

Integrates expression data and applies computational algorithms to systematically predict miRNA–enhancer–gene trios.