ReNE

ReNE enhances gene-based regulatory networks as a Cytoscape 3.x plugin by incorporating transcriptional, post-transcriptional, and translational data to provide detailed representations of regulatory mechanisms.

Key Features:

• Automatic Network Enrichment: Enriches gene-based regulatory networks with transcription factors, miRNAs, and proteins to represent multiple regulatory layers.
• Integration from Multiple Sources: Integrates pathways and interactions from repositories such as Reactome and KEGG and accepts custom pathways described in OWL/XML.
• Pathway Merging and Normalization: Merges pathways from different origins into a single network and normalizes node and edge descriptions for consistent representation.
• Annotation Enrichment: Retrieves and attaches additional annotations from genome-wide databases such as NCBI to integrated network entities.
• Visualization and Export Capabilities: Preserves regulatory element types (transcription factors, miRNAs, genes, proteins) and regulatory mechanisms (up-regulation, down-regulation) within Cytoscape and supports export in multiple formats for third-party analysis.

Scientific Applications:

• Regulatory mechanism analysis: Enables inclusion of post-transcriptional regulators such as miRNAs into gene-based networks to analyze multilayer regulatory interactions.
• Systems biology: Supports construction of integrated networks for system-level modeling of regulatory processes.
• Genomics: Facilitates interpretation of regulatory interactions in genomic studies by adding transcriptional and translational details.
• Personalized medicine: Provides enriched regulatory networks that can be used to investigate cell-specific regulatory mechanisms relevant to personalized analyses.

Methodology:

Imports network layouts from established repositories or custom OWL/XML pathways, merges these with additional data sources (e.g., Reactome, KEGG), normalizes node and edge descriptions, enriches networks with transcription factors, miRNAs, proteins and annotations from genome-wide databases such as NCBI, and relies on public repository data for introduced interactions.