iPTMnet visualization with Cytoscape Web

Ren, Jia
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University of Delaware
iPTMnet is a new bioinformatics resource for post-translational modifications (PTMs). It integrates text mining, data mining, databases and ontologies into one convenient platform. These large collections of relations are important tools for studying specific cell behaviors. Data visualization is an effective methodology to make sense of thousands of rows of data. The graphic presentation is able to highlight important substructures. We use Cytoscape Web, a web-based graphic presentation platform, to build a visualization tool for iPTMnet. Several web visualization tools have been built with Cytoscape Web to facilitate projects target on showing proteinprotein interaction, predicting related gene group, and integrating protein-protein interaction, chromatin machinery and human disease. Here we present a novel graphic presentation of the iPTMnet. The motivation of the thesis work is to assist researchers in quickly identifying PTM for one or agroup of Protein Ontology (PRO) entries. In this work, we mainly focus on PRO curated PTM relations and visualize PRO hierarchy structure, proteinprotein interactions, phosphorylation and acetylation. We tackled problems in storing and presenting hierarchy structure, creating a user-friendly interface and constructing view functions. The visualization tool is used to support a spindle checkpoint study and help reveal the evolutionary relationship, perform cross-species comparison to predict phosphorylation site, and construct PPI network.