DbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications

Zhongyan Li; Shangfu Li; Mengqi Luo; Jhih Hua Jhong; Wenshuo Li; Lantian Yao; Yuxuan Pang; Zhuo Wang; Rulan Wang; Renfei Ma; Jinhan Yu; Yuqi Huang; Xiaoning Zhu; Qifan Cheng; Hexiang Feng; Jiahong Zhang; Chunxuan Wang; Justin Bo Kai Hsu; Wen Chi Chang; Feng Xiang Wei; Hsien Da Huang; Tzong Yi Lee

doi:10.1093/nar/gkab1017

DbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications

Zhongyan Li, Shangfu Li, Mengqi Luo, Jhih Hua Jhong, Wenshuo Li, Lantian Yao, Yuxuan Pang, Zhuo Wang, Rulan Wang, Renfei Ma, Jinhan Yu, Yuqi Huang, Xiaoning Zhu, Qifan Cheng, Hexiang Feng, Jiahong Zhang, Chunxuan Wang, Justin Bo Kai Hsu, Wen Chi Chang, Feng Xiang Wei^*Hsien Da Huang^*, Tzong Yi Lee^*

^*Corresponding author for this work

Institute of Bioinformatics and Systems Biology

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

82 Scopus citations

Abstract

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

Original language	English
Pages (from-to)	D471-D479
Journal	Nucleic acids research
Volume	50
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkab1017
State	Published - 7 Jan 2022

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Li, Z., Li, S., Luo, M., Jhong, J. H., Li, W., Yao, L., Pang, Y., Wang, Z., Wang, R., Ma, R., Yu, J., Huang, Y., Zhu, X., Cheng, Q., Feng, H., Zhang, J., Wang, C., Hsu, J. B. K., Chang, W. C., ... Lee, T. Y. (2022). DbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic acids research, 50(D1), D471-D479. https://doi.org/10.1093/nar/gkab1017

@article{0cd4237782eb47cd957e7d0824744419,

title = "DbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications",

abstract = "Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.",

author = "Zhongyan Li and Shangfu Li and Mengqi Luo and Jhong, {Jhih Hua} and Wenshuo Li and Lantian Yao and Yuxuan Pang and Zhuo Wang and Rulan Wang and Renfei Ma and Jinhan Yu and Yuqi Huang and Xiaoning Zhu and Qifan Cheng and Hexiang Feng and Jiahong Zhang and Chunxuan Wang and Hsu, {Justin Bo Kai} and Chang, {Wen Chi} and Wei, {Feng Xiang} and Huang, {Hsien Da} and Lee, {Tzong Yi}",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2022",

month = jan,

day = "7",

doi = "10.1093/nar/gkab1017",

language = "English",

volume = "50",

pages = "D471--D479",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Li, Z, Li, S, Luo, M, Jhong, JH, Li, W, Yao, L, Pang, Y, Wang, Z, Wang, R, Ma, R, Yu, J, Huang, Y, Zhu, X, Cheng, Q, Feng, H, Zhang, J, Wang, C, Hsu, JBK, Chang, WC, Wei, FX, Huang, HD & Lee, TY 2022, 'DbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications', Nucleic acids research, vol. 50, no. D1, pp. D471-D479. https://doi.org/10.1093/nar/gkab1017

TY - JOUR

T1 - DbPTM in 2022

T2 - An updated database for exploring regulatory networks and functional associations of protein post-translational modifications

AU - Li, Zhongyan

AU - Li, Shangfu

AU - Luo, Mengqi

AU - Jhong, Jhih Hua

AU - Li, Wenshuo

AU - Yao, Lantian

AU - Pang, Yuxuan

AU - Wang, Zhuo

AU - Wang, Rulan

AU - Ma, Renfei

AU - Yu, Jinhan

AU - Huang, Yuqi

AU - Zhu, Xiaoning

AU - Cheng, Qifan

AU - Feng, Hexiang

AU - Zhang, Jiahong

AU - Wang, Chunxuan

AU - Hsu, Justin Bo Kai

AU - Chang, Wen Chi

AU - Wei, Feng Xiang

AU - Huang, Hsien Da

AU - Lee, Tzong Yi

PY - 2022/1/7

Y1 - 2022/1/7

N2 - Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

AB - Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

UR - http://www.scopus.com/inward/record.url?scp=85123388476&partnerID=8YFLogxK

U2 - 10.1093/nar/gkab1017

DO - 10.1093/nar/gkab1017

M3 - Article

C2 - 34788852

AN - SCOPUS:85123388476

SN - 0305-1048

VL - 50

SP - D471-D479

JO - Nucleic acids research

JF - Nucleic acids research

IS - D1

ER -

DbPTM in 2022: An updated database for exploring regulatory networks and functional associations of protein post-translational modifications

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