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. 2023 Jan 1;39(1):btac823.
doi: 10.1093/bioinformatics/btac823.

PTMint database of experimentally verified PTM regulation on protein-protein interaction

Xiaokun Hong  1 , Ningshan Li  2 , Jiyang Lv  1 , Yan Zhang  1 , Jing Li  1 , Jian Zhang  3 , Hai-Feng Chen  1
Affiliations

PTMint database of experimentally verified PTM regulation on protein-protein interaction

Xiaokun Hong et al. Bioinformatics. .

Abstract

Motivation: Post-translational modification (PTM) is an important biochemical process. which includes six most well-studied types: phosphorylation, acetylation, methylation, sumoylation, ubiquitylation and glycosylation. PTM is involved in various cell signaling pathways and biological processes. Abnormal PTM status is closely associated with severe diseases (such as cancer and neurologic diseases) by regulating protein functions, such as protein-protein interactions (PPIs). A set of databases was constructed separately for PTM sites and PPI; however, the resource of regulation for PTM on PPI is still unsolved.

Results: Here, we firstly constructed a public accessible database of PTMint (PTMs that are associated with PPIs) (https://ptmint.sjtu.edu.cn/) that contains manually curated complete experimental evidence of the PTM regulation on PPIs in multiple organisms, including Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Currently, the first version of PTMint encompassed 2477 non-redundant PTM sites in 1169 proteins affecting 2371 protein-protein pairs involving 357 diseases. Various annotations were systematically integrated, such as protein sequence, structure properties and protein complex analysis. PTMint database can help to insight into disease mechanism, disease diagnosis and drug discovery associated with PTM and PPI.

Availability and implementation: PTMint is freely available at: https://ptmint.sjtu.edu.cn/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
The overall design and construction of PTMint database
Fig. 2.
Fig. 2.
The data in the PTMint database. Statistical analysis results in terms of PTM types (A) and PTM sites (B). (C) Top 10 diseases affected by PTM. (D) PTM-associated PPI network. Top 10 genes with highest degrees were highlighted in PPI (D) and visualized in bar plot (E)
Fig. 3.
Fig. 3.
The detailed information in PTMint database. (A) Browse function. (B) Search_function. (C) The returned search results using the CTDP1 as an example. The entry page consists of six major sections: (1) Protein overview. (2) Protein features. (3) PTM on PPIs. (4) Interaction network. Blue square: gene, Green circle: Int_gene, Red arrow: from gene to int_gene interaction. (5) Importance score of PTM sites and (6) complex analysis (A color version of this figure appears in the online version of this article)
See this image and copyright information in PMC

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