PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways

Introduction:A central element of cellular signaling are protein post-translational modifications (PTMs). Upon a perturbation such as a drug treatment, many proteins undergo a change on PTM level, which can have fundamental consequences for the phenotype. While PTM data nowadays is routinely acquired, it is still hard to interpret the regulated PTMs in the context of signaling cascades. Here, we present PTMNavigator, a web-based software tool to explore PTM proteomics datasets from a pathway-centric viewpoint. Our software is able to render pathway diagrams interactively and project experimental PTM data onto them. A number of enrichment analyses can be performed to identify the most relevant pathways, gene sets, and kinases for a dataset. The tool is hosted on ProteomicsDB (proteomicsdb.org/analytics/ptmNavigator), and users can either browse through what is available there or upload their own data.

Methods:PTMNavigator was developed as a Vue.js application. The core visualization component is a WebComponent (github.com/kusterlab/biowc-pathwaygraph). A set of canonical pathway diagrams was created in ProteomicsDB by importing pathways of 10 model organisms from KEGG and WikiPathways. To perform enrichment analyses, a Flask-based web service was implemented. PTMNavigator integrates the visualization and enrichment results together with additional information (e.g. from PhosphoSitePlus) in a web platform.

Results:Users of our tool can choose from the ~3,000 available pathway diagrams and project their PTM data onto them. In addition, they can create their own diagrams to visualize bespoke interactions. Multiple functional enrichment algorithms (e.g. PTM-SEA, KSEA) are automatically run after data upload and the results are summarized in PTMNavigator. The results are also used to score and rank the canonical pathways to facilitate manual inspection. Optionally, kinase-substrate relationships from PhosphoSitePlus can be visualized as additional links in the pathway diagrams. Also, the software PHONEMeS is used to construct a data-driven signaling network using prior knowledge from STRING and PhosphoSitePlus. Visualizations can be exported to create publication-level figures with ease. Using a number of recently published datasets, we demonstrated some applications of our software. First, we showed how pathway visualization and enrichment analysis can be combined to find out which pathways are actually relevant for a dataset. Second, we visualized how kinase inhibitors with different targets perturb the PI3K/AKT/mTOR phospho-signaling cascade at different stages. Third, PTMNavigator helped us to extend an existing pathway by uncovering previously unknown relationships between PTMs and pathway components.

Conclusion:We present an easy-to-use web tool for the study of PTM signaling networks. To our knowledge, PTMNavigator is the first tool that enables comprehensive and in-depth pathway-centric analyses of PTM datasets within a single application.