Glydin' : the Glycoepitope Network
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Motivation
Glycan determinants, also called glycoepitopes, have been collected by different authors and recorded in different ways in a few unrelated databases or simply printed in tables of articles. In all cases, glycoepitopes are listed as independent entities despite their compositional similarity and the common set of enzymes required to synthesise them.
We designed Glydin’ (Glycan Dynamics) to (1) merge the distinct sources describing glycoepitopes in different formats and (2) map the similarity between these entities in an interactive network. Glydin’ is as a result, a tool to visualise and explore the relationships between glycoepitopes based on either their shared monosaccharide composition or the glycosyltransferase needed to get one from the other.
What’s inside?
This epitope network was produced using four different sources:- The table referenced in R. Cummings’ 2009 review, a reference in the field
- The BiOligo section of the Glyco3D database maintained at Cermav
- A manually curated version of the GlycoEpitope database (contributed by Dr Catherine Hayes)
- SugarBindDB
Glydin’ displays glycoepitopes as nodes in a network. Two networks are mapped to emphasise two different types of shared properties:
In the “Substructure Based Map”, two nodes are connected if one glycoepitope is a substructure of the other.
In the “Enzyme Base Map”, two nodes are connected as the result of a glycosyltransferase adding a monosaccharide to the other.
In the “Substructure Based Map”, the network is one large connected component whereas in the “Enzyme Base Map” it is a collection of connected components each stemming from a single monosaccharide.
As a result, the “Substructure Based Map” shows connections between a trimer and a pentamer if the former is part of the latter while the “Enzyme Base Map” only connects structures differing of one or possibly two monosaccharides when two identical monosaccharides are added with the same linkage. This the case for example, of core 4 (GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc(a-) that becomes 3,6-(LacNAc)2Tn (Gal(b1-4)GlcNAc(b1-3)[Gal(b1-4)GlcNAc(b1-6)]GalNAc(a-) through the action of β4Gal-T4 that adds 2 galactoses with a beta4 linkage on each branch of the core 4 structure.
How to:
Browse the networks
The following list of actions can be performed on the network:- Hover over a node will prompt the glycoepitope name and highlight neighbouring glycoepitopes.
- Click once on a node to see the glycoepitope details in the upper right window. In this window, the structure is displayed along with active links to the sources where the glycoepitope was described and active links to neighbouring glycoepitopes in the network. In other words, clicking on the link to a related glycoepitope will move to that glycoepitope.
- Double click on a node to visualise a single glycoepitope with the nodes connected to it.
- Click on the target icon to centre the network on the selected glycoepitope.
- Zoom in and out on the network with the “+” and “- “ signs:
- If you zoom in when centred on an epitope, the network will expand around it
- Below a certain zoom level, glycoepitope names are automatically displayed for all the nodes.
Search for a specific glycoepitope
A glycoepitope can be searched by name in any displayed network. The user can input text in the search window and Glydin’ will support this input with auto-completion. Then, clicking on the search button will fade all the nodes except the searched glycoepitope. The upper right window will be updated to show information regarding the searched glycoepitope.Browse results of EpitopeXtractor
When using EpitopeXtractor, the user is automatically directed to the Glydin’ display of results. The actions are exactly the same as those described above for browsing the networks. However, in this case, navigation is guided by red-coloured nodes that represent the mapping of all glycoepitopes selected by EpitopeXtractor.Reference
If you use Glydin' please cite:Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes. Alocci D. et al, Glycobiology. 2018. (PubMed Id: 29518231)