NETGE-PLUS

NETGE-PLUS performs standard and network-based functional enrichment analyses of gene sets to interpret omics data and elucidate genotype-phenotype relationships across human and model organisms including Sus scrofa, Saccharomyces cerevisiae, Escherichia coli, and Arabidopsis thaliana.

Key Features:

• Enrichment modes: Implements both standard and network-based enrichment analyses for functional interpretation of gene sets.
• Organism support: Supports human genes and model organisms including Sus scrofa, Saccharomyces cerevisiae, Escherichia coli, and Arabidopsis thaliana.
• Input types: Accepts simple (unranked) gene lists and ranked gene lists as input.
• KEGG pathway integration: Explores relationships among KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways to integrate pathway-based insights into gene set interpretation.
• Omics-driven interpretation: Leverages omics data to characterize complex traits at the molecular level and elucidate genotype-phenotype relationships.

Scientific Applications:

• Functional interpretation: Interprets functional roles of gene sets derived from omics experiments.
• Cross-species analysis: Supports functional analyses of human genes and genes from model organisms (Sus scrofa, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana).
• Complex trait characterization: Aids characterization of complex traits at the molecular level using omics-derived gene sets.
• Pathway-context analysis: Elucidates relationships among KEGG pathways to provide pathway-based context for phenotype associations.

Methodology:

Performs standard and network-based functional enrichment analyses on simple or ranked gene lists and explores relationships among KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways.