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

Area of Science:

• Molecular Biology
• Proteomics
• Systems Biology

Background:

• Post-translational modifications (PTMs) are crucial for regulating cellular signaling and protein function.
• Current tools lack a pathway-centric approach for studying PTMs, hindering understanding of their role in cellular processes.
• Investigating PTMs in the context of signaling pathways is essential for deciphering complex biological mechanisms.

Purpose of the Study:

• To introduce PTMNavigator, an integrated tool for visualizing experimental PTM data alongside canonical and custom pathway diagrams.
• To provide researchers with an interactive platform for exploring PTM-mediated cellular signaling.
• To facilitate the discovery of PTM-pathway interactions and their implications in health and disease.

Main Methods:

• PTMNavigator integrates experimental PTM data with ~3000 canonical pathways from curated databases within the ProteomicsDB platform.
• Users can modify existing pathway diagrams or create custom ones tailored to their specific experimental data.
• The tool automatically performs kinase and pathway enrichment analyses, with results directly visualized within the pathway context.

Main Results:

• PTMNavigator enables a comprehensive visualization of the interplay between PTMs and signaling pathways.
• Application to phosphoproteomics datasets demonstrated enhanced pathway enrichment analysis.
• The tool effectively visualizes drug treatment effects on PTM-driven signaling and aids in pathway extension hypotheses.

Conclusions:

• PTMNavigator enhances the understanding of cellular signaling dynamics by providing a pathway-centric view of PTMs.
• It facilitates the discovery of novel PTM-pathway interactions, advancing PTM biology.
• The tool has significant implications for research in health and disease, aiding in the interpretation of complex biological data.