IntramiRExploreR

IntramiRExploreR integrates predicted miRNA–mRNA binding information and microarray expression evidence to identify and prioritize targets of intragenic microRNAs in Drosophila melanogaster.

Key Features:

• Intragenic miRNA target identification: Systematically identifies targets of intragenic miRNAs in Drosophila melanogaster.
• Binding prediction: Uses sequence/biophysical interaction models to predict miRNA–mRNA binding.
• Expression integration: Incorporates observed expression patterns across Affymetrix 1 and Affymetrix 2 microarray platforms.
• Functional grouping: Groups predicted targets using the DAVID Gene Ontology system to assess enriched biological processes, molecular functions, and cellular components.
• Scoring and ranking: Ranks candidate targets with a biologically motivated scoring scheme combining interaction strength, expression concordance, and functional context.
• Systems-level analysis: Leverages genome-wide expression profiles to provide a global view of intragenic miRNA–mRNA regulatory relationships.

Scientific Applications:

• Target discovery in Drosophila: Systematic identification of intragenic miRNA targets in Drosophila melanogaster.
• Prioritization of functional interactions: Prioritizes miRNA–mRNA interactions supported by both binding evidence and coherent expression changes.
• Functional enrichment analysis: Facilitates assessment of enriched GO terms using the DAVID Gene Ontology system.
• Hypothesis generation: Supports generation of hypotheses about intragenic miRNA roles in Drosophila development, physiology, and disease.

Methodology:

Integrates predicted miRNA–mRNA binding from sequence/biophysical interaction models with observed expression patterns from Affymetrix 1 and Affymetrix 2 microarray datasets, groups targets using the DAVID Gene Ontology system, and ranks candidates using a scoring scheme that combines interaction strength, expression concordance, and functional context.