NIH Proteomics Interest Group

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ProtIG is an NIH Special Interest Group (SIG) that organizes seminars and workshops in relevant areas of proteomics, including talks on separation and protein identification methods, determination of post-translational modifications, protein-protein interactions, and bioinformatics and data management. A monthly seminar series is held at 10am usually on the first Thursday of each month (always check the Mtgs/Seminars button on this page for these and other PROTIG announced meetings). To receive email announcements of ProtIG events, join the listserv (Join the SIG button on this page)

April ProtIG Seminar
April 2, 2015
10:00am - 11:00pm
Building 50, NIH Campus
Room 1227/1233 (first floor lobby)
Cathy Wu, Ph.D.
Edward G. Jefferson Chair and Professor and Director of the Center for Bioinformatics & Computational Biology (CBCB), University of Delaware
Director of the Protein Information Resource(PIR) and the North east Bioinformatics Collaborative Steering Committee
Adjunct Professor at the Georgetown University Medical Center

"Construction of Protein PTM Networks by Data Mining, Text Mining, and Ontology Integration: Application to Multi-Faceted Disease Analysis"

Perturbations in post-translational modifications (PTMs) and their downstream effects are recognized as key drivers of disease. We have developed iPTMnet, employing an integrative bioinformatics approach—combining text mining, data mining, and ontological representation to capture rich PTM information—for PTM network and disease discovery. Text mining tools are used for full-scale mining of PubMed abstracts and PMC Open Access articles to identify PTM information (kinase, substrate, and site) and phosphorylation-dependent protein-protein interactions (PPIs) in their biological context, including disease consequences. Experimentally observed PTMs, including high-throughput proteomic data from curated PTM databases, are incorporated. Ontologies are used for knowledge representation, particularly the Protein Ontology (PRO) for representation of PTM proteoforms and complexes. The web portal ( supports online search and visual analysis, including multiple-sequence alignment views for comparison of PTM forms across organisms and Cytoscape visualization of PTM enzyme-substrate and PPI relationships in PTM interaction networks. We are conducting use cases for PTM-disease discovery. First, we analyzed phosphorylation-dependent PPIs related to the PI3K/AKT/mTOR pathway, which is deregulated in many cancers and is targeted by therapeutic kinase inhibitors. We classified interactions as pro- and anti-oncogenic to indicate potential mechanisms of kinase-inhibitor resistance. Second, we made a knowledge map of beta-catenin PTM proteoforms to interpret patterns of mutations in PTM sites occurring in different types of cancer, revealing multiple mechanisms through which mutations in beta-catenin PTM sites contribute to cancer. Finally, we are exploring the phosphorylation of pyruvate dehydrogenase (PDHA1), a mediator of the Warburg effect in cancer whose phosphorylation levels span a 64-fold range in breast cancer patient samples from phosphoproteomic data CPTAC. We are investigating the levels and activity of PDHA1 kinases and phosphatases in the same samples using genomic, transcriptomic (mRNA and miRNA), and proteomic data to gain insight into the efficacy of existing anti-cancer drugs that target PDHA1 phosphorylation.

Seminars will be webcast online at and available on the
Proteomics Interest Group website as an archived presentation unless otherwise noted.

Please remember everyone is welcome to join us for the Fellows Forum Seminar on the 9th of April (in Building 10, Room 3-2550). See the Fellows Forum for more information.

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This site was updated on March 24th, 2015. Please contact Renee Olano at olanol(at) with questions or suggestions.