Zhou Yusen, Ghosh Vishnu, Venkatesan Shriramprasad, Sriram Shyam, Sobczak Edward, Setlur Srirangaraj, Gunawan Rudiyanto, Neelamegham Sriram
Department of Chemical & Biological Engineering, State University of New York, Buffalo, NY 14260.
Department of Computer Science and Engineering, State University of New York, Buffalo, NY 14260.
bioRxiv. 2025 Aug 31:2025.08.30.673257. doi: 10.1101/2025.08.30.673257.
The glycan distribution on cells is governed by the stochastic activity of different families of enzymes that are together called 'glycoEnzymes'. These include ~400 gene products or 2% of the proteome, that have recently been curated in an ontology called GlycoEnzOnto. With the goal of making this ontology more accessible to the larger biomedical and biotechnology community, we organized a web resource called GlycoEnzDB, presenting this enzyme classification both in terms of enzyme function and the pathways that they participate in. This information is linked to i) Figures from the " Essentials of Glycobiology" textbook, ii) General gene, enzyme and pathway data appearing in external databases, iii) Manual and generative-artificial intelligence (AI) based text describing the function and pathways regulated by these entities, iv) Single-cell expression data across cell lines, normal human cell-types and tissue, and v) CRISPR-knockout/activation/inactivation and Transcription factor activity predictions. Whereas these data are curated for human glycoEnzymes, the knowledge framework may be extended to other species also. The user-friendly web interface is accessible at www.virtualglycome.org/glycoenzdb.
细胞上的聚糖分布由不同酶家族的随机活性决定,这些酶统称为“糖酶”。它们包括约400种基因产物,占蛋白质组的2%,最近已在一个名为GlycoEnzOnto的本体中进行了整理。为了使这个本体更容易被更广泛的生物医学和生物技术社区所使用,我们组织了一个名为GlycoEnzDB的网络资源,从酶功能及其参与的途径两个方面展示这种酶分类。这些信息与以下内容相关联:i)《糖生物学基础》教科书中的图表;ii)外部数据库中出现的一般基因、酶和途径数据;iii)基于人工手动和生成式人工智能(AI)描述这些实体调控的功能和途径的文本;iv)跨细胞系、正常人类细胞类型和组织的单细胞表达数据;v)CRISPR基因敲除/激活/失活以及转录因子活性预测。虽然这些数据是针对人类糖酶整理的,但该知识框架也可扩展到其他物种。用户友好的网络界面可在www.virtualglycome.org/glycoenzdb访问。