PPIExp: A Web-Based Platform for Integration and Visualization of Protein–Protein Interaction Data and Spatiotemporal Proteomics Data

Integrating spatiotemporal
proteomics data with protein–protein
interaction (PPI) data can help researchers make an in-depth exploration
of their proteins of interest in a dynamic manner. However, there
is still a lack of proper tools for the biologists who usually have
few programming skills to construct a PPI network for a protein list,
visualize active PPI subnetworks, and then select key nodes for further
study. We propose a web-based platform named PPIExp that can automatically
construct a PPI network, perform clustering analysis according to
protein abundances, and perform functional enrichment analysis. More
importantly, it provides multiple effective visualization interfaces,
such as the interface to display the PPI network map, the interface
to display a dendrogram and heatmap for the clustering result, and
the interface to display the expression pattern of a selected protein.
To visualize the active PPI subnetworks in specific space or time,
it provides buttons to highlight the differentially expressed proteins
under each condition on the network map. Additionally, to help researchers
determine which proteins are worth further attention, PPIExp provides
extensive one-click interactive operations to map node centrality
measures to node size on the network and highlight three types of
proteins, that is, the proteins in an enriched functional term, the
coexpressed proteins selected from the dendgrogram and heatmap, and
the proteins input by users. PPIExp is available at http://www.fgvis.com/expressvis/PPIExp.