dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research

Area of Science:

• Biochemistry
• Bioinformatics
• Genomics

Background:

• Post-translational modifications (PTMs) are crucial for protein function, stability, activity, and signaling.
• The dbPTM database serves as a vital resource for PTM information.

Purpose of the Study:

• To present the significant expansion and new features of the dbPTM 2025 database update.
• To highlight the integration of cancer-specific proteomic data and regulatory networks.
• To enhance the utility of dbPTM for cancer research and the study of disease-associated PTMs.

Main Methods:

• Expansion of the dbPTM database to include over 2.79 million PTM sites (2.243 million experimentally validated).
• Integration of proteomic data from 13 cancer types, focusing on phosphoproteomics and kinase activity.
• Incorporation of kinase-substrate phosphorylations and E3 ligase-substrate interactions to map PTM regulatory networks.
• Development of advanced search capabilities, interactive visualization tools, and streamlined data downloads.

Main Results:

• dbPTM 2025 now contains over 2.79 million PTM sites, with 2.243 million experimentally validated.
• The database integrates extensive cancer proteomic data, enabling personalized phosphorylation pattern analysis in tumors.
• New features facilitate efficient data querying, analysis, and exploration of PTM regulatory networks.
• Enhanced functional annotations, regulatory networks, and disease associations are provided.

Conclusions:

• dbPTM 2025 is a comprehensive and user-friendly resource for studying PTMs.
• The updated database significantly advances cancer research by providing detailed insights into PTMs and their regulatory networks.
• dbPTM 2025 facilitates the investigation of disease-associated PTMs and personalized cancer therapies.