PolygenicPathways

PolygenicPathways analyzes interactions among genes, environmental risk factors, autoantibodies, and pathogens (including herpes simplex virus, Helicobacter pylori, and HIV-1/AIDS) in polygenic diseases and maps susceptibility genes to KEGG pathways to characterize host–pathogen interactions.

Key Features:

• Gene-Pathway Analysis: Integrates gene datasets with KEGG pathway mapping to characterize roles in neurotransmission, neuroplasticity, oligodendrocyte function, and other neurobiological processes.
• Host-Pathogen Interaction Characterization: Identifies gene involvement in pathogen life cycles and host–pathogen interactions, including examples such as AGA metabolizing viral ligands, EGFR facilitating CMV entry, and FGFR1 usage by herpes simplex virus.
• Viral Traffic Regulation: Examines genes such as DISC1, DTNBP1, and BLOC1S3 that regulate microtubule networks and endosomal-to-lysosomal trafficking relevant to viral trafficking.
• Immune Response Genes: Analyzes innate and adaptive immune genes including CCR5, IL10, and HLA antigens for their roles in defense against pathogens.
• MicroRNA Interactions: Predicts interactions between human microRNAs (e.g., Hsa-mir-198, Hsa-mir-206) and viral genes to infer post-transcriptional regulatory mechanisms.

Scientific Applications:

• Disease Mechanism Elucidation: Maps gene–pathogen interactions to investigate molecular underpinnings of diseases such as schizophrenia where pathogen presence may influence genetic associations.
• Therapeutic Target Identification: Uses pathogen–gene interaction insights to suggest potential targets for drugs or vaccines that disrupt pathogenic interactions with susceptibility genes.
• Population Studies: Provides a framework to assess heterogeneity in genetic studies of polygenic diseases by incorporating pathogen prevalence as a variable across populations and time.

Methodology:

Integrates genomic data with KEGG pathway analysis to map gene functions and interactions and characterizes host–pathogen dynamics.