ArticlePLoS computational biology2016
A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 41 citations in OpenAlex.
- Glycan reachability analysis: A bottleneck-aware framework for inferring tissue-specific glycan biosynthetic potential from transcriptomics.PLoS computational biology · 2026Article
- Glycosyltransferases: glycoengineers in human milk oligosaccharide synthesis and manufacturing.Frontiers in molecular biosciences · 2025Review
- In silico simulation of glycosylation and related pathways.Analytical and bioanalytical chemistry · 2024Review
- Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens.Scientific reports · 2024Article
- UniCarb-DB: An MS/MS Experimental Glycomic Fragmentation Database.Methods in molecular biology (Clifton, N.J.) · 2024Article
- In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis.Scientific reports · 2022Article
- Article
- Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration.Nature communications · 2022Article
- Computational Modeling ofMolecules (Basel, Switzerland) · 2022Article
- O-Glycologue: A Formal-Language-Based Generator of O-Glycosylation Networks.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An Interactive View of Glycosylation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comparative Glycomics Analysis of Mass Spectrometry Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication.Trends in biochemical sciences · 2021Review
- Simulating the enzymes of ganglioside biosynthesis with Glycologue.Beilstein journal of organic chemistry · 2021Article
- A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering.Current research in biotechnology · 2020Article
- Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching.Molecular & cellular proteomics : MCP · 2020Article
- A consensus-based and readable extension ofBeilstein journal of organic chemistry · 2020Article
- A mechanism for bistability in glycosylation.PLoS computational biology · 2018Article
- Multi-level regulation of cellular glycosylation: from genes to transcript to enzyme to structure.Current opinion in structural biology · 2016Review
- Fc gamma receptors: glycobiology and therapeutic prospects.Journal of inflammation research · 2016Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
O-linked glycosylation is an important post-translational modification of mucin-type protein, changes to which are important biomarkers of cancer. For this study of the enzymes of O-glycosylation, we developed a shorthand notation for representing GalNAc-linked oligosaccharides, a method for their graphical interpretation, and a pattern-matching algorithm that generates networks of enzyme-catalysed reactions. Software for generating glycans from the enzyme activities is presented, and is also available online. The degree distributions of the resulting enzyme-reaction networks were found to be Poisson in nature. Simple graph-theoretic measures were used to characterise the resulting reaction networks. From a study of in-silico single-enzyme knockouts of each of 25 enzymes known to be involved in mucin O-glycan biosynthesis, six of them, β-1,4-galactosyltransferase (β4Gal-T4), four glycosyltransferases and one sulfotransferase, play the dominant role in determining O-glycan heterogeneity. In the absence of β4Gal-T4, all Lewis X, sialyl-Lewis X, Lewis Y and Sda/Cad glycoforms were eliminated, in contrast to knockouts of the N-acetylglucosaminyltransferases, which did not affect the relative abundances of O-glycans expressing these epitopes. A set of 244 experimentally determined mucin-type O-glycans obtained from the literature was used to validate the method, which was able to predict up to 98% of the most common structures obtained from human and engineered CHO cell glycoforms.
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