miRTrail

miRTrail analyzes interactions between microRNAs (miRNAs) and their predicted target genes using mRNA transcripts to elucidate regulatory mechanisms in complex diseases.

Key Features:

• Integrative Analysis: Integrates mRNA and miRNA expression profiles to identify deregulated pathogenic processes and regulatory interactions.
• Extensive Database Integration: Incorporates datasets covering approximately 20,000 genes, nearly 1,000 miRNAs, and around 280,000 putative gene-miRNA interactions for Homo sapiens, Mus musculus, and Danio rerio.
• Gene and miRNA Set Analysis: Performs analyses on gene sets and miRNA sets individually or in combination using a systems biology approach.
• Statistical Techniques: Employs the classical Chi-squared test to jointly consider miRNAs and their target genes.
• Interactive Visualization: Provides network visualization of results via network analyzers and viewers such as BiNA and Cytoscape-web with access to relevant literature.
• Application Evidence: Has been used to identify deregulated miRNAs such as hsa-miR-23b and hsa-miR-223 that target numerous deregulated mRNAs involved in oncogenic pathways like basal cell carcinoma.
• Versatility with Data Types: Compatible with microarray-based expression profiles and next-generation sequencing (NGS)-based transcriptomic data.

Scientific Applications:

• Cancer research: Identification of deregulated miRNAs and target mRNAs involved in oncogenic pathways, exemplified by analyses of basal cell carcinoma.
• Comparative and model organism studies: Analysis of gene–miRNA interactions across Homo sapiens, Mus musculus, and Danio rerio for comparative biology.
• Transcriptomic integration: Joint analysis of microarray and NGS expression profiles to study regulatory networks in genetics and systems biology.

Methodology:

Integrates mRNA and miRNA expression profiles, uses a database of gene–miRNA interactions, performs gene and miRNA set analyses, applies the classical Chi-squared test for joint consideration of miRNAs and target genes, and visualizes results with BiNA or Cytoscape-web.