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基于网络的工具整合,以可视化、整合和解释糖基因表达和糖组学数据。

Integration of Web-Based Tools to Visualize, Integrate, and Interpret Glycogene Expression and Glycomics Data.

机构信息

CardiOmics Program, Center for Heart and Vascular Research, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA.

出版信息

Methods Mol Biol. 2024;2836:97-109. doi: 10.1007/978-1-0716-4007-4_7.

Abstract

Glycosylation is the most abundant and diverse post-translational modification occurring on proteins. Glycans play important roles in modulating cell adhesion, growth, development, and differentiation. Changes in glycosylation affect protein structure and function and contribute to disease processes. Therefore, understanding glycosylation patterns is key for the identification of targets for the diagnosis of diseases, cellular states, and therapy. Glycosylation is a non template-driven process governed by the action of numerous enzymes and substrate availability that varies among cell types and species. Therefore, qualitative and quantitative assessment of global glycosylation and individual glycans remains challenging because it requires integration of multiple complex data types. Glycan structure and quantity data are often integrated with assessments of gene expression to aid contextualization of observed glycosylation changes within biological processes. However, correlating glycogene expression to the glycan structure is challenging because transcriptional changes may not always concur with the final gene product; there is often a lack of information on nucleotide sugar pools, and the final glycan structure is the result of many different glycogenes acting in concert. To overcome these challenges, interactive online tools are emerging as key resources for facilitating the analysis and integration of glycomics and glycogene expression data. Importantly, these tools work in concurrence with glycan biosynthetic schemes and therefore provide a clear indication of the molecular pathways where the glycan and glycogene are involved. In this chapter, we describe the applications of four freely available online tools that can be used for integrated visualization, interpretation, and presentation of RNAseq and glycomics results.

摘要

糖基化是蛋白质上最丰富和最多样化的翻译后修饰。聚糖在调节细胞黏附、生长、发育和分化方面发挥着重要作用。糖基化的变化影响蛋白质的结构和功能,并导致疾病过程。因此,了解糖基化模式是识别疾病、细胞状态和治疗靶点的关键。糖基化是一个非模板驱动的过程,由多种酶的作用和底物的可用性决定,而这些在不同的细胞类型和物种中有所不同。因此,对全局糖基化和单个糖链的定性和定量评估仍然具有挑战性,因为它需要整合多种复杂的数据类型。糖链结构和数量数据通常与基因表达评估相结合,以帮助在生物过程中对观察到的糖基化变化进行背景化。然而,将糖基因表达与糖链结构相关联具有挑战性,因为转录变化并不总是与最终的基因产物一致;核苷酸糖池的信息往往缺乏,并且最终的糖链结构是许多不同的糖基因协同作用的结果。为了克服这些挑战,交互式在线工具作为促进糖组学和糖基因表达数据分析和整合的关键资源正在出现。重要的是,这些工具与糖生物合成方案同时工作,因此可以清楚地表明糖和糖基因参与的分子途径。在本章中,我们描述了四个免费在线工具的应用,这些工具可用于 RNAseq 和糖组学结果的综合可视化、解释和呈现。

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本文引用的文献

1
Increasing Complexity of the N-Glycome During Caenorhabditis Development.
Mol Cell Proteomics. 2023 Mar;22(3):100505. doi: 10.1016/j.mcpro.2023.100505. Epub 2023 Jan 28.
2
The known unknowns of apolipoprotein glycosylation in health and disease.
iScience. 2022 Aug 28;25(9):105031. doi: 10.1016/j.isci.2022.105031. eCollection 2022 Sep 16.
3
Applying transcriptomics to studyglycosylation at the cell type level.
iScience. 2022 May 18;25(6):104419. doi: 10.1016/j.isci.2022.104419. eCollection 2022 Jun 17.
5
Integrated analysis of glycan and RNA in single cells.
iScience. 2021 Jul 17;24(8):102882. doi: 10.1016/j.isci.2021.102882. eCollection 2021 Aug 20.
6
Global mapping of glycosylation pathways in human-derived cells.
Dev Cell. 2021 Apr 19;56(8):1195-1209.e7. doi: 10.1016/j.devcel.2021.02.023. Epub 2021 Mar 16.
7
Characterization and statistical modeling of glycosylation changes in sickle cell disease.
Blood Adv. 2021 Mar 9;5(5):1463-1473. doi: 10.1182/bloodadvances.2020003376.
8
SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells.
Sci Adv. 2021 Feb 19;7(8). doi: 10.1126/sciadv.abe3610. Print 2021 Feb.
9
Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor.
Mol Cell Proteomics. 2020 Oct;19(10):1602-1618. doi: 10.1074/mcp.RA120.002041. Epub 2020 Jul 7.
10
Distinct glycosylation in membrane proteins within neonatal versus adult myocardial tissue.
Matrix Biol. 2020 Jan;85-86:173-188. doi: 10.1016/j.matbio.2019.05.001. Epub 2019 May 17.

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