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

Julian Müller, Florian P. Bayer, Mathias Wilhelm, Maximilian G. Schuh, Bernhard Kuster and Matthew The ()
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Julian Müller: Technical University of Munich
Florian P. Bayer: Technical University of Munich
Mathias Wilhelm: Technical University of Munich
Maximilian G. Schuh: Technical University of Munich
Bernhard Kuster: Technical University of Munich
Matthew The: Technical University of Munich

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform that offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams. PTMNavigator provides ~3000 canonical pathways from manually curated databases, enabling users to modify and create custom diagrams tailored to their data. Additionally, PTMNavigator automatically runs kinase and pathway enrichment algorithms whose results are directly integrated into the visualization. This offers a comprehensive view of the intricate relationship between PTMs and signaling pathways. We demonstrate the utility of PTMNavigator by applying it to two phosphoproteomics datasets, showing how it can enhance pathway enrichment analysis, visualize how drug treatments result in a discernable flow of PTM-driven signaling, and aid in proposing extensions to existing pathways. By enhancing our understanding of cellular signaling dynamics and facilitating the discovery of PTM-pathway interactions, PTMNavigator advances our knowledge of PTM biology and its implications in health and disease.

Date: 2025
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DOI: 10.1038/s41467-024-55533-y

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