P0304
iPTMnet: An Integrated Resource for Protein Post-Translational Modification Network Discovery

Jung-Youn Lee , Plant and Soil Sciences – University of Delaware, Newark, DE
Hongzhan Huang , Center Bioinformatics & Comp Bio – University of Delaware, Newark, DE
Jia Ren , University of Delaware, Newark, DE
Cecilia Arighi , CBCB – University of Delaware, Newark, DE
Karen Ross , Georgetown University Medical Ctr., Washington, DC
Gang Li , Center Bioinformatics & Comp Bio – University of Delaware, Newark, DE
Catalina Oana Tudor Tudor , Center Bioinformatics & Comp Bio – University of Delaware, Newark, DE
Mengxi LV , University of Delaware, Newark, DE
Vijay Shanker , University of Delaware, Newark, DE
Cathy H. Wu , CBCB, University of Delaware, Newark, DE
To address gaps in the current resources available for analysis of post-translational modification (PTM) networks, we have developed iPTMnet, an integrated resource for protein post-translational modification network discovery in the systems biology context. iPTMnet integrates high quality PTM information from multiple sources covering phosphorylation, acetylation, glycosylation, methylation, myristoylation, sumoylation and ubiquitylation in a range of organisms. We employ our RLIMS-P/eFIP text mining system to extract kinase, substrate, and site relations as well as mentions of phosphorylation dependent protein-protein interactions (PPIs) from the scientific literature. These results are combined with information from manually curated PTM databases. Proteins and PTM protein forms (proteoforms) are organized using the Protein Ontology (PRO), enabling representation of forms modified on combinations of PTM sites and orthologous relationships between forms.  The iPTMnet database contains more than 250,000 PTM sites in more than 45,000 modified proteins, along with more than 1,000 PTM enzymes for human, mouse, yeast, Arabidopsis and other organisms. The web interface links the underlying system components to support interactive scientific queries and visualization of PTM information. Example of iPTMnet queries include: i) finding the PTM substrates for a given PTM enzyme; ii) finding PTM sites for a given protein; iii) finding the PTM enzymes that modify a protein; iv) comparing modified sites and proteoforms for a given protein; v) finding phospho-dependent PPIs, vi) visualizing modification sites in an alignment of a protein across species, including known proteoforms; and vii) visualizing networks of PTM-enzyme/substrate relations along with sites, proteoforms and phospho-dependent PPIs.
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