title: PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks.
abstract: Post-translational modifications of proteins (PTMs) act as key regulators of protein activity and of protein-protein interactions (PPIs). To date, it has been difficult to comprehensively explore functional links between PTMs and PPIs. To address this, we developed PTMOracle, a Cytoscape app for coanalyzing PTMs within PPI networks. PTMOracle also allows extensive data to be integrated and coanalyzed with PPI networks, allowing the role of domains, motifs, and disordered regions to be considered. For proteins of interest, or a whole proteome, PTMOracle can generate network visualizations to reveal complex PTM-associated relationships. This is assisted by OraclePainter for coloring proteins by modifications, OracleTools for network analytics, and OracleResults for exploring tabulated findings. To illustrate the use of PTMOracle, we investigate PTM-associated relationships and their role in PPIs in four case studies. In the yeast interactome and its rich set of PTMs, we construct and explore histone-associated and domain-domain interaction networks and show how integrative approaches can predict kinases involved in phosphodegrons. In the human interactome, a phosphotyrosine-associated network is analyzed but highlights the sparse nature of human PPI networks and lack of PTM-associated data. PTMOracle is open source and available at the Cytoscape app store: http://apps.cytoscape.org/apps/ptmoracle .
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia.
authors.forename: Aidan P
authors.identifier: 0000-0003-1315-4896
authors.initials: AP
authors.lastname: Tay
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia.
authors.forename: Chi Nam Ignatius
authors.identifier: 0000-0001-9703-5741
authors.initials: CNI
authors.lastname: Pang
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Winter
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia.
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
mesh_terms: D005656:Fungal Proteins; D006801:Humans; D063731:Mobile Applications; D010770:Phosphotransferases / Q000378:metabolism; D019000:Phosphotyrosine / Q000378:metabolism; D060066:Protein Interaction Maps; D011499:Protein Processing, Post-Translational; D011506:Proteins; D015003:Yeasts
chemical_list: D005656:Fungal Proteins; D011506:Proteins; D019000:Phosphotyrosine; D010770:Phosphotransferases
keywords: Cytoscape; data integration; networks; post-translational modification; protein−protein interaction; visualization