Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes

Abstract

Nowadays, due to the advance of experimental techniques in glycomics, large collections of glycan profiles are regularly published. The rapid growth of available glycan data accentuates the lack of innovative tools for visualizing and exploring large amount of information. Scientists resort to using general-purpose spreadsheet applications to create ad hoc data visualization. Thus, results end up being encoded in publication images and text, while valuable curated data is stored in files as supplementary information. To tackle this problem, we have built an interactive pipeline composed with three tools: Glynsight, EpitopeXtractor and Glydin'. Glycan profile data can be imported in Glynsight, which generates a custom interactive glycan profile. Several profiles can be compared and glycan composition is integrated with structural data stored in databases. Glycan structures of interest can then be sent to EpitopeXtractor to perform a glycoepitope extraction. EpitopeXtractor results can be superimposed on the Glydin' glycoepitope network. The network visualization allows fast detection of clusters of glycoepitopes and discovery of potential new targets. Each of these tools is standalone or can be used in conjunction with the others, depending on the data and the specific interest of the user. All the tools composing this pipeline are part of the Glycomics@ExPASy initiative and are available at https://www.expasy.org/glycomics.

Comparative Glycomics of Immunoglobulin A and G From Saliva and Plasma Reveals Biomarker Potential

“…This further complicates detailed (S)IgA glycosylation analysis. However, in recent years great progress has been made with respect to both measurement sensitivity and data analysis tools in the field of glycoproteomics, facilitating site-specific glycosylation analysis of minute amounts of Igs ( 29 – 32 ).…”

Glycomics@ExPASy: Bridging the Gap

“…To keep both the number of databases and their extent to a minimum, the glyco-epitope collection is made accessible only through applications. As detailed in ( 37 ) it results from the compilation of four independent sources (GlycoEpitopeDB, SugarBindDB, Glyco3D ( 38 ) and the literature) and the glycoepitopes were all translated into the GlycoCT format. Glycan array binding data were downloaded from the Consortium for Functional Glycomics (CFG) database ( http://www.functionalglycomics.org/glycomics/publicdata/ ) to reinforce the lectin recognition described in SugarBindDB.…”

A Review on Computational Tools and Databases for the Development of Vaccines Against Infectious Diseases

“…[21] Glydin' GlyDyn'is an investigation system to explore the connections between epitopes based on monosaccharide composition. [22] The server gives a graphical representation of the Epitope Network.…”