Reference: Y. Zhou, V. Ghosh, et al., "GlycoEnzDB: A database of enzymes involved in mammalian glycosylation", in preparation, 2024.
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 been recently curated in an ontology called GlycoEnzOnto (Groth et al., Bioinformatics, 38(24): 5413–5420, 2022). With the goal of making this ontology more accessible to the larger biomedical and biotechnology community, we organized a web resource 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 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.
This repository contains all data files and code used to develop the django web resource. THe following are the locations of relevant data files
GlycoEnzOntoDB: describes hierarchy of otology used in website
Scripts used to pull generic enzyme data from Uniprot
gpt text created using Dr. Glyco GPT
reaction_imgs/: enzyme reaction
pathway_figures/: pathway figures used in rendering
CCLE data
Tabula Sapiens ssingle cell transcriptomics data parsed for the glycogenes
CRISPRa/: figures for CRISPR activation
CRISPRi/: figures for CRISPR inactivation
CRISPRko/: figures for CRISPR knockout
Transcription Factor - Glycogene interaction figures in all formats
Final rendered files are in webGlycoEnzDB/djangoProject/data/html600
Licensing: CC BY 4.0. You are fee to copy, redistribute, remix, transform and build upon this material for commercial and non-commercial purposes, provided source of information is attributed/credited.