MAGIA2

MAGIA2 performs integrative analysis of in silico target predictions, microRNA (miRNA) and gene expression data to reconstruct post-transcriptional regulatory networks and mixed miRNA–transcription factor circuits.

Key Features:

• Target Prediction Integration: Integrates target predictions from algorithms including PITA, miRanda, and Target Scan and supports Boolean combinations of these predictions.
• Multistep Analysis Procedure: Integrates mRNA and miRNA expression data using parametric and non-parametric correlation indexes, a variational Bayesian model, mutual information, and a meta-analysis based on P-value combination.
• Network Construction: Constructs bipartite regulatory networks of the best putative miRNA–mRNA interactions.
• Data Retrieval and Literature Mining: Retrieves information from public databases on genes, miRNAs, and diseases and performs scientific literature text-mining.
• Mixed Regulatory Circuit Reconstruction: Identifies two types of regulatory circuits: a transcription factor that regulates both a miRNA and its target, and a miRNA that regulates both a transcription factor and its target.
• Support for Multiple Organisms: Supports analysis of data from multiple organisms.

Scientific Applications:

• miRNA regulatory network reconstruction: Reconstructs post-transcriptional regulatory networks to analyze miRNA-mediated gene regulation.
• Refinement of miRNA target predictions: Combines target-prediction algorithms with expression profiles to refine target predictions and address low specificity of individual algorithms.
• Mixed TF–miRNA circuit analysis: Identifies and characterizes mixed regulatory circuits involving transcription factors and miRNAs to dissect multi-layer regulatory interactions.

Methodology:

Uses Boolean combinations of target-prediction algorithms (PITA, miRanda, Target Scan), computes parametric and non-parametric correlation indexes, applies a variational Bayesian model, estimates mutual information, employs a meta-analysis based on P-value combination, reconstructs bipartite miRNA–mRNA networks, identifies mixed TF–miRNA regulatory circuits, and performs literature text-mining and public-database retrieval.