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PPIExp: a web-based platform for integration and visualization of protein-protein interaction data and spatiotemporal proteomics data.

Research paper by Xian X Liu, Cheng C Chang, Mingfei M Han, Ronghua R Yin, Yiqun Y Zhan, Changyan C Li, Changhui C Ge, Miao M Yu, Xiaoming X Yang

Indexed on: 20 Dec '18Published on: 20 Dec '18Published in: Journal of Proteome Research



Abstract

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. Here, we propose a web-based platform named PPIExp, which 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 & 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 in 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, i.e., the proteins in an enriched functional term, the co-expressed proteins selected from the dendgrogram & heatmap, and the proteins input by users. PPIExp is available at http://www.fgvis.com/expressvis/PPIExp.