RENATO

Renato: Regulatory Network Analysis for Transcription Factors and microRNAs

Renato analyzes transcriptional and post-transcriptional regulatory networks by mapping gene lists to transcription factors (TFs) and microRNAs (miRNAs) within a regulatory network database and identifying significantly associated regulators.

Key Features:

• Regulatory Network Exploration: Extracts and evaluates regulatory connections to assess functional modularity and network integrity under specific perturbations.
• Gene List Analysis: Identifies TFs or miRNAs compatible with gene activation or deactivation using single enrichment and gene set enrichment tests.
• Over-Representation Evaluation: Maps input genes to the regulatory network and tests each regulator for significant over-representation within the gene list.
• Ranked Gene List Analysis: Analyzes ranked gene lists to assess regulator significance relative to gene hierarchy or expression levels.

Scientific Applications:

• Gene Regulation Studies: Identifies TF and miRNA regulators in expression profiling, disease models, developmental biology, and functional genomics studies involving network perturbations.

Methodology:

Maps input genes onto a curated regulatory network database, extracts corresponding TF–gene and miRNA–gene interactions, and applies statistical enrichment analyses to evaluate regulator over-representation and significance within the query gene set.