OGP: A Repository of Experimentally Characterized O-glycoproteins to Facilitate Studies on O-glycosylation.

Jiangming Huang, Mengxi Wu, Yang Zhang, Siyuan Kong, Mingqi Liu, Biyun Jiang, Pengyuan Yang, Weiqian Cao

Abstract read

In one paragraph

Article in Genomics, proteomics & bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it

0cells of the map it votes in

12citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

UniPTMs: a unified multi-type PTM site prediction model via master-slave architecture-based multi-stage fusion strategy and hierarchical contrastive loss.BMC bioinformatics · 2026
Article
GalNAc-T13 maintains neurite architecture and memory retention via O-GalNAc glycosylation of seizure protein 6.Proceedings of the National Academy of Sciences of the United States of America · 2026
Article
UniGraphPTMs: a contrastive learning-enhanced universal framework for PTM site prediction via GNN and multimodal fusion.BMC genomics · 2026
Article
Next-generation protein sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6.Analytical and bioanalytical chemistry · 2025
Article
Sitetack: a deep learning model that improves PTM prediction by using known PTMs.Bioinformatics (Oxford, England) · 2024
Article
Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model.Bioinformatics (Oxford, England) · 2024
Article
Polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) isozyme surface charge governs charge substrate preferences to modulate mucin type O-glycosylation.Glycobiology · 2023
Article
Quantitative mapping of the in vivo O-GalNAc glycoproteome in mouse tissues identifies GalNAc-T2 O-glycosites in metabolic disorder.Proceedings of the National Academy of Sciences of the United States of America · 2023
Article
TNFα-induced metabolic reprogramming drives an intrinsic anti-viral state.PLoS pathogens · 2022
Article
Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4-pRB Axis in Fibroblasts at the Invasive Tumor Edge.Cancer research · 2022
Article
An analytical study on the identification of N-linked glycosylation sites using machine learning model.PeerJ. Computer science · 2022
Article
Glycobiology and proteomics: has mass spectrometry moved the field forward?Expert review of proteomics
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Jiangming HuangDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai 200032, China.

Mengxi WuDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai 200032, China.

Yang ZhangDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai 200032, China.

Siyuan KongDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

Mingqi LiuDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

Biyun JiangDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai 200032, China.

Pengyuan YangDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai 200032, China; NHC Key Laboratory of Glycoconjugates Research (Fudan University), Shanghai 200032, China. Electronic address: pyyang@fudan.edu.cn.

Weiqian CaoDepartment of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai 200032, China; NHC Key Laboratory of Glycoconjugates Research (Fudan University), Shanghai 200032, China. Electronic address: wqcao@fudan.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Numerous studies on cancers, biopharmaceuticals, and clinical trials have necessitated comprehensive and precise analysis of protein O-glycosylation. However, the lack of updated and convenient databases deters the storage of and reference to emerging O-glycoprotein data. To resolve this issue, an O-glycoprotein repository named OGP was established in this work. It was constructed with a collection of O-glycoprotein data from different sources. OGP contains 9354 O-glycosylation sites and 11,633 site-specific O-glycans mapping to 2133 O-glycoproteins, and it is the largest O-glycoprotein repository thus far. Based on the recorded O-glycosylation sites, an O-glycosylation site prediction tool was developed. Moreover, an OGP-based website is already available (https://www.oglyp.org/). The website comprises four specially designed and user-friendly modules: statistical analysis, database search, site prediction, and data submission. The first version of OGP repository and the website allow users to obtain various O-glycoprotein-related information, such as protein accession Nos., O-glycosylation sites, O-glycopeptide sequences, site-specific O-glycan structures, experimental methods, and potential O-glycosylation sites. O-glycosylation data mining can be performed efficiently on this website, which will greatly facilitate related studies. In addition, the database is accessible from OGP website (https://www.oglyp.org/download.php).

Indexed as

GlycoproteinsDatabases, ProteinGlycosylationGlycoproteinsData miningO-glycoprotein related websiteO-glycoprotein repositoryO-glycosylationSite prediction

Identifiers

PMID33581334

DOI10.1016/j.gpb.2020.05.003

PMCPMC9039567

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.