psygenet2r

psygenet2r provides R functions to retrieve and analyze PsyGeNET psychiatric disorder–gene association data for network-based, comorbidity, gene expression and molecular-function analyses.

Key Features:

• Data Retrieval: Accesses PsyGeNET database records of psychiatric disorders and their associated genes.
• Comorbidity Analysis: Integrates PsyGeNET curated data with user-provided datasets to perform comorbidity and disease–disease relationship analyses.
• Query Capabilities: Supports configurable queries to extract disease–gene associations from PsyGeNET.
• Analysis Tools: Provides functions to analyze gene expression across anatomical structures and to characterize molecular functions of associated genes.
• Visualization Tools: Generates graphical representations of genetic networks and pathways.

Scientific Applications:

• Network Medicine: Facilitates network medicine approaches to study psychiatric disorders using disease–gene association networks from PsyGeNET.
• Mechanism and Target Discovery: Enables identification of candidate therapeutic targets and investigation of disease etiology through integrated genomic and network analyses.
• Translational and Personalized Research: Supports translational research and personalized medicine strategies by integrating genomic and comorbidity data.

Methodology:

Implemented in R, psygenet2r retrieves and integrates PsyGeNET data—a resource produced by text mining and expert curation—to perform network-based analyses, comorbidity integration, gene expression assessment across anatomical structures, and molecular-function characterization.