ProdoNet

ProdoNet maps prokaryotic genes and their encoded proteins onto gene regulatory and metabolic networks to identify shared operons, co-expressed genes and joint regulators and to visualize their contributions on KEGG metabolic maps.

Key Features:

• Gene-to-network mapping: Maps prokaryotic genes and proteins onto common gene regulatory and metabolic networks.
• Operon and co-expression detection: Identifies shared operons, co-expressed genes, and joint regulators from an input gene list.
• Expression integration: Incorporates gene expression profiles into global network visualizations to aid interpretation of transcriptomics and proteomics data.
• KEGG pathway visualization: Maps gene contributions onto KEGG metabolic pathway maps.
• Regulatory dataset integration: Uses the PRODORIC Prokaryotic Database of Gene Regulation and the Virtual Footprint tool for transcriptional regulation data.

Scientific Applications:

• Regulatory and metabolic context mapping: Determine regulatory and metabolic contexts for prokaryotic genes and proteins.
• Transcriptomics and proteomics interpretation: Overlay expression data on regulatory and metabolic networks to interpret transcriptomics and proteomics experiments.
• Operon and co-expression analysis: Detect operons, co-expression modules, and shared regulators among gene sets.
• Pathway contribution analysis: Visualize how specific genes contribute to shared metabolic pathways via KEGG maps.
• Proteome study case: Applied to analysis of an experimental membrane subproteome in Pseudomonas aeruginosa.

Methodology:

Accepts an input list of genes, systematically identifies shared operons, co-expressed genes and joint regulators, integrates these elements with gene expression profiles, and maps the results onto KEGG metabolic maps using transcriptional regulation data derived from PRODORIC and Virtual Footprint.