NETMAGE

NETMAGE generates disease-disease networks from summarized Phenome-Wide Association Study (PheWAS) results by representing phenotypes as nodes and shared genetic associations as edges to enable analysis of pleiotropy and shared genetic architecture.

Key Features:

• Network construction: Constructs disease-disease networks from summarized PheWAS results with nodes representing distinct phenotypes and edges representing shared genetic associations.
• SNP mapping: Maps single nucleotide polymorphisms (SNPs) to associated phenotypes and records shared SNP associations between phenotypes.
• Pleiotropy identification: Detects instances where single genetic loci are associated with multiple phenotypic traits.
• Dataset compatibility: Supports analysis using PheWAS summary data such as UK Biobank PheWAS summary results.
• Network statistics: Computes and reports network-level metrics and phenotype-relationship statistics derived from shared genetic associations.

Scientific Applications:

• Pleiotropy discovery: Identification of pleiotropic loci influencing multiple phenotypes from PheWAS summary data.
• Shared genetic architecture analysis: Exploration of genetic overlap and relationships among phenotypic traits.
• Hypothesis generation for genomic research: Prioritization of shared genetic components for downstream studies, including potential target identification.

Methodology:

Integrates summarized PheWAS results by mapping phenotypic traits as network nodes and establishing edges based on shared genetic associations, including shared SNP associations, then derives network statistics.