DICP: Development of a web tool for predicting the glycan structures in human cells
- Database Integration Coordination Program
Professor Kiyoko Kinoshita of Soka University has developed a web tool for glycochain research, "GlycoMaple" in collaboration with Jiangnan University of China and the University of Georgia in U.S.A. The results of verifying the validity and reliability of this tool were reported in Developmental Cell on March 16, 2021.
GlycoMaple is a web tool for visualization of the expression profile of 950 genes concerning glycan biosynthesis, and for predicting the glycan structures synthesized in the cells. It is opened in "GlyCosmos Portal".
The latest discoveries in glycan biosynthesis and metabolism were collected from the literatures and databases, and categorized to construct GlycoMaple. Validity and reliability of the prediction by GlycoMaple were validated with engineered HEK293 cells in which glycan-related genes were overexpressed or knocked out. Changes of glycan structures associated with carcinogenesis in intestine predicted by GlycoMaple with TCGA (The Cancer Genome Atlas) and GTEx (Genotype-Tissue Expression) data were well concorded with known glycan structures reported in the colorectal cancer patient specimens.
There are some limitations, such as this tool being non-quantitative and the prediction is not individual glycan structure of each protein but those potentially synthesized in the cells. However, it should be usefull not only for basic research of studying glycan structures or regulatory mechanisms but also for developing glycoprotein medicines and glycan biomarkers.
GlyCosmos Portal and GlycoMaple were developed in the project "Construction of a Glycoscience Portal" (Principal Investigator: Kiyoko Kinoshita) funded by the Database Integration Coordination Program (DICP), NBDC.
For details, see the original publication and the press release published by Soka University.
- Original report (March 16, 2021), Yi-Fan Huang, et al., Global mapping of glycosylation pathways in human-derived cells. Developmental Cell (2021)(DOI: 10.1016/j.devcel.2021.02.023).
- Press release by Soka University (March 16, 2021)
- Funded projects "Construction of a Glycoscience Portal"
- GlyCosmos Portal | Integbio Database Catalog
Summary of GlyCosmos Portal.