Pathwayscan

Pathwayscan is a hypothetical open-source software tool designed for pathway analysis in genomics and proteomics. It provides a framework to scan omics datasets for enrichment and connectivity within metabolic and signaling pathways, enabling researchers to interpret large-scale data in biological context.

Features include a modular pipeline for data preprocessing, identifier harmonization across gene and protein databases, support for multiple pathway databases (e.g., KEGG, Reactome, WikiPathways), enrichment scoring using over-representation analysis and network-based methods, and visualization of results on pathway diagrams and interaction networks. The tool emphasizes reproducibility with configurable parameters and support for common file formats (CSV/TSV, GMT/GPX, JSON).

Workflow: import data; map to standard identifiers; select pathway libraries; compute pathway scores; assess significance with multiple-testing correction; generate reports and visualizations; export results for downstream tools such as Cytoscape. The software is designed to be extensible via plugins or scripts.

Applications: interpretation of differential expression, functional genomics studies, cross-omics integration, and comparative pathway analysis across species or conditions.

Development and licensing: Pathwayscan is presented here as a generic example of a pathway-scanning framework typical in bioinformatics, often released under permissive licenses to encourage academic use. See also: Pathway analysis, gene set enrichment analysis, Cytoscape, KEGG, Reactome, WikiPathways.