PPIExp

PPIExp constructs protein-protein interaction (PPI) networks and integrates protein abundance data to identify coexpressed clusters, perform functional enrichment, and visualize active subnetworks across conditions and time points.

Key Features:

• Automatic Construction of PPI Networks: Generates PPI networks from input protein lists to enable initial network analysis.
• Clustering Analysis Based on Protein Abundances: Performs clustering analyses using protein abundance data to identify coexpressed protein groups.
• Functional Enrichment Analysis: Conducts functional enrichment analysis to determine the biological significance of proteins or clusters within the network.
• Dynamic Visualization Interfaces: Produces PPI network maps, dendrogram and heatmap displays for clustering results, and expression pattern visualizations for selected proteins.
• Highlighting Active PPI Subnetworks: Identifies and highlights subnetworks enriched for differentially expressed proteins under specific conditions.
• Interactive Operations: Maps node centrality measures to node size and highlights proteins within enriched functional terms or coexpressed clusters.
• User-Defined Protein Highlighting: Highlights user-specified proteins within networks for targeted analysis.

Scientific Applications:

• Spatiotemporal proteomics integration: Integrates spatiotemporal proteomics data with PPI information to explore functional dynamics across conditions and time points.
• Systems biology: Supports systems biology investigations by revealing interaction patterns and coexpression modules within protein networks.
• Disease mechanism studies: Facilitates analysis of disease mechanisms by identifying active subnetworks and differentially expressed proteins.
• Drug discovery: Aids drug discovery by pinpointing central or functionally enriched proteins as potential targets.

Methodology:

Automates PPI network construction and visualization using computational techniques; clustering and enrichment analyses apply statistical methods that incorporate protein abundance data.