cisPath

cisPath provides R/Bioconductor-based functionality to construct, integrate, manage, and visualize functional protein-protein interaction (PPI) networks for proteomics and systems biology analyses.

Key Features:

• Implementation: Implemented as an R/Bioconductor package to operate within R-based bioinformatics workflows.
• Integration with Online Databases: Integrates PPI data downloaded from multiple online databases with private datasets to build comprehensive interaction networks.
• Dynamic Network Construction: Offers functions to generate specific PPI networks based on user-defined criteria using private databases.
• Network Visualization: Provides functionality to visualize and manipulate network graphs representing PPI relationships.
• Network Management: Includes functions to manage and store functional PPI networks for downstream analysis.

Scientific Applications:

• Pathway analysis: Elucidating complex biological pathways by mapping protein interactions.
• Drug target identification: Identifying potential drug targets through analysis of interaction networks.
• Disease mechanism exploration: Exploring molecular mechanisms underlying various diseases via network-level interaction analysis.
• Proteomics and systems biology: Supporting comprehensive analyses that integrate diverse datasets and network-level information.

Methodology:

Implemented in R/Bioconductor with functions to integrate PPI data from multiple online databases and private datasets, construct PPI networks based on user-defined criteria, and visualize/manage resulting network graphs.