DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research

Chia Ru Chung; Yun Tang; Yen Peng Chiu; Shangfu Li; Wen Kai Hsieh; Lantian Yao; Ying Chih Chiang; Yuxuan Pang; Guan Ting Chen; Kai Chen Chou; You Sheng Paik; Phuong Lam Tran; Cheng Pei Lin; Yu Min Kao; Yi Jie Chen; Wen Chi Chang; Justin Bo Kai Hsu; Jorng Tzong Horng; Tzong Yi Lee

doi:10.1093/nar/gkae1005

DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research

Chia Ru Chung, Yun Tang, Yen Peng Chiu, Shangfu Li, Wen Kai Hsieh, Lantian Yao, Ying Chih Chiang, Yuxuan Pang, Guan Ting Chen, Kai Chen Chou, You Sheng Paik, Phuong Lam Tran, Cheng Pei Lin, Yu Min Kao, Yi Jie Chen, Wen Chi Chang, Justin Bo Kai Hsu^*, Jorng Tzong Horng^*, Tzong Yi Lee^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.243 million are experimentally validated from 48 databases and over 80 000 research articles. This version integrates proteomic data from 13 cancer types, with a particular focus on phosphoproteomic data and kinase activity profiles, allowing the exploration of personalized phosphorylation patterns in tumor samples. Integrating kinase-substrate phosphorylations with E3 ligase-substrate interactions, dbPTM 2025 provides a detailed map of PTM regulatory networks, offering insights into cancer-specific post-translational regulations. This update also includes advanced search capabilities, enabling users to efficiently query PTM data across species, PTM types and modified residues. The platform's new features - interactive visualization tools and streamlined data downloads - allow researchers to access and analyze PTM data easily. dbPTM 2025 also enhances functional annotations, regulatory networks and disease associations, broadening its application for cancer research and the study of disease-associated PTMs. Through these enhancements, dbPTM 2025 is a comprehensive, user-friendly resource, facilitating the study of PTMs and their roles in cancer research. The database is now freely accessible at https://biomics.lab.nycu.edu.tw/dbPTM/.

Original language	English
Pages (from-to)	D377-D386
Journal	Nucleic acids research
Volume	53
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkae1005
State	Published - 6 Jan 2025

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Chung, C. R., Tang, Y., Chiu, Y. P., Li, S., Hsieh, W. K., Yao, L., Chiang, Y. C., Pang, Y., Chen, G. T., Chou, K. C., Paik, Y. S., Tran, P. L., Lin, C. P., Kao, Y. M., Chen, Y. J., Chang, W. C., Hsu, J. B. K., Horng, J. T., & Lee, T. Y. (2025). DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research. Nucleic acids research, 53(D1), D377-D386. https://doi.org/10.1093/nar/gkae1005

@article{32657df964b6427d8d6ee415e117371a,

title = "DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research",

abstract = "Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.243 million are experimentally validated from 48 databases and over 80 000 research articles. This version integrates proteomic data from 13 cancer types, with a particular focus on phosphoproteomic data and kinase activity profiles, allowing the exploration of personalized phosphorylation patterns in tumor samples. Integrating kinase-substrate phosphorylations with E3 ligase-substrate interactions, dbPTM 2025 provides a detailed map of PTM regulatory networks, offering insights into cancer-specific post-translational regulations. This update also includes advanced search capabilities, enabling users to efficiently query PTM data across species, PTM types and modified residues. The platform's new features - interactive visualization tools and streamlined data downloads - allow researchers to access and analyze PTM data easily. dbPTM 2025 also enhances functional annotations, regulatory networks and disease associations, broadening its application for cancer research and the study of disease-associated PTMs. Through these enhancements, dbPTM 2025 is a comprehensive, user-friendly resource, facilitating the study of PTMs and their roles in cancer research. The database is now freely accessible at https://biomics.lab.nycu.edu.tw/dbPTM/.",

author = "Chung, {Chia Ru} and Yun Tang and Chiu, {Yen Peng} and Shangfu Li and Hsieh, {Wen Kai} and Lantian Yao and Chiang, {Ying Chih} and Yuxuan Pang and Chen, {Guan Ting} and Chou, {Kai Chen} and Paik, {You Sheng} and Tran, {Phuong Lam} and Lin, {Cheng Pei} and Kao, {Yu Min} and Chen, {Yi Jie} and Chang, {Wen Chi} and Hsu, {Justin Bo Kai} and Horng, {Jorng Tzong} and Lee, {Tzong Yi}",

note = "Publisher Copyright: {\textcopyright} 2025 The Author(s) 2024.",

year = "2025",

month = jan,

day = "6",

doi = "10.1093/nar/gkae1005",

language = "English",

volume = "53",

pages = "D377--D386",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

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Chung, CR, Tang, Y, Chiu, YP, Li, S, Hsieh, WK, Yao, L, Chiang, YC, Pang, Y, Chen, GT, Chou, KC, Paik, YS, Tran, PL, Lin, CP, Kao, YM, Chen, YJ, Chang, WC, Hsu, JBK, Horng, JT & Lee, TY 2025, 'DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research', Nucleic acids research, vol. 53, no. D1, pp. D377-D386. https://doi.org/10.1093/nar/gkae1005

TY - JOUR

T1 - DbPTM 2025 update

T2 - Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research

AU - Chung, Chia Ru

AU - Tang, Yun

AU - Chiu, Yen Peng

AU - Li, Shangfu

AU - Hsieh, Wen Kai

AU - Yao, Lantian

AU - Chiang, Ying Chih

AU - Pang, Yuxuan

AU - Chen, Guan Ting

AU - Chou, Kai Chen

AU - Paik, You Sheng

AU - Tran, Phuong Lam

AU - Lin, Cheng Pei

AU - Kao, Yu Min

AU - Chen, Yi Jie

AU - Chang, Wen Chi

AU - Hsu, Justin Bo Kai

AU - Horng, Jorng Tzong

AU - Lee, Tzong Yi

PY - 2025/1/6

Y1 - 2025/1/6

N2 - Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.243 million are experimentally validated from 48 databases and over 80 000 research articles. This version integrates proteomic data from 13 cancer types, with a particular focus on phosphoproteomic data and kinase activity profiles, allowing the exploration of personalized phosphorylation patterns in tumor samples. Integrating kinase-substrate phosphorylations with E3 ligase-substrate interactions, dbPTM 2025 provides a detailed map of PTM regulatory networks, offering insights into cancer-specific post-translational regulations. This update also includes advanced search capabilities, enabling users to efficiently query PTM data across species, PTM types and modified residues. The platform's new features - interactive visualization tools and streamlined data downloads - allow researchers to access and analyze PTM data easily. dbPTM 2025 also enhances functional annotations, regulatory networks and disease associations, broadening its application for cancer research and the study of disease-associated PTMs. Through these enhancements, dbPTM 2025 is a comprehensive, user-friendly resource, facilitating the study of PTMs and their roles in cancer research. The database is now freely accessible at https://biomics.lab.nycu.edu.tw/dbPTM/.

AB - Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.243 million are experimentally validated from 48 databases and over 80 000 research articles. This version integrates proteomic data from 13 cancer types, with a particular focus on phosphoproteomic data and kinase activity profiles, allowing the exploration of personalized phosphorylation patterns in tumor samples. Integrating kinase-substrate phosphorylations with E3 ligase-substrate interactions, dbPTM 2025 provides a detailed map of PTM regulatory networks, offering insights into cancer-specific post-translational regulations. This update also includes advanced search capabilities, enabling users to efficiently query PTM data across species, PTM types and modified residues. The platform's new features - interactive visualization tools and streamlined data downloads - allow researchers to access and analyze PTM data easily. dbPTM 2025 also enhances functional annotations, regulatory networks and disease associations, broadening its application for cancer research and the study of disease-associated PTMs. Through these enhancements, dbPTM 2025 is a comprehensive, user-friendly resource, facilitating the study of PTMs and their roles in cancer research. The database is now freely accessible at https://biomics.lab.nycu.edu.tw/dbPTM/.

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U2 - 10.1093/nar/gkae1005

DO - 10.1093/nar/gkae1005

M3 - Article

C2 - 39526378

AN - SCOPUS:85214584972

SN - 0305-1048

VL - 53

SP - D377-D386

JO - Nucleic acids research

JF - Nucleic acids research

IS - D1

ER -

DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research

Abstract

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