GlyConnect is a platform designed to investigate the relationships between glycans, the proteins that carry them and the proteins that bind them via the UniLectin sister project. The underlying database stores curated data on glycosylation extracted from literature and preserving the contextual information relative to species, original cell line, tissue and disease.
GlyConnect is the central resource of the Glyco@Expasy collection hosted at SIB - Swiss Institute of Bioinformatics.
Usage of the GlyConnect platform is illustrated in this tutorial video:
GlyConnect data is licenced under CC-BY-4.0.
GlyConnect and Octopus: Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F (2019) GlyConnect: glycoproteomics goes visual, interactive and analytical, Software tools and data resources Special issue of J Prot Research 18(2):664-677.
Glycomics@ExPASy: Mariethoz J, Alocci D, Gastaldello A, Horlacher O, Gasteiger E, Rojas-Macias MA, Karlsson NG, Packer NH, Lisacek F (2018) Glycomics@ExPASy: Bridging the gap, Mol Cell Proteomics 17: 2164–2176.
Compozitor: Robin T, Mariethoz J, Lisacek F (2020) Examining and fine-tuning the selection of glycan compositions with GlyConnect Compozitor, Mol Cell Proteomics.
GlycoSiteAlign: Gastaldello A, Alocci D, Baeriswyl JL, Mariethoz J, Lisacek F (2016) GlycoSiteAlign: Glycosite Alignment Based on Glycan Structure, J Proteome Res.15(10):3916-3928.
Glydin’ and Glynsight: Alocci D, Ghraichy M, Barletta E, Gastaldello A, Mariethoz J, Lisacek F (2018) Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes., Glycobiology 28(6):349-362.
The platform described in the article cited above was substantially modified in the September 2020 release. The Browse and Search sections have been merged, the octopus has been redesigned and a new broader filtering tool has been implemented to browse the data. The homepage reflects these conceptual changes.
GlyConnect can be searched as a catalogue of glycosylated proteins in their specific context or as a collection of links between entities of the database (octopus) reflects these conceptual changes.
The platform described in the article cited above was substantially modified in the September 2020 release. The Browse and Search sections have been merged, the octopus has been redesigned and a new broader filtering tool has been implemented to browse the data. The homepage reflects these conceptual changes.
The catalogue is accessible by categories of entities represented as coloured buttons. Pressing on either of these will output the list of the corresponding entities. For example, with this tool you can answer questions such as:
By clicking on the orange PROTEIN button that prompts the display of all glycoprotein names along with their cross-references in other databases and the details of where they are found . This list can be reduced to items of interest by entering relevant terms in the Filter box. In the example questions, here are the answers:
In all cases, items of the list have links that open on further information and references are systematically provided as supporting evidence.
Along the same line, clicking on the green TISSUE button of the homepage prompts the display of all tissue names (controlled vocabulary) and the associated glycoconjugates. As an example the term “mucosa” typed in the filter window will shortlist all tissue names containing mucosa,e.g., mucosa of stomach, colonic mucosa. From the complete or a filtered list, each item is associated with a series of coloured buttons with values matching the corresponding content in the database. For instance, the blue STRUCTURE button shows information on all structures reported in the tissue named in the first column.
As a last example, peptide sequences supported by mass spectrometry evidence can be listed and filtered by an instance of a sequon, e.g., NFT, in an N-glycoprotein.
Further details on how the filtering tool works are provided below each Filter box.
Because lists do not reveal relationships between entities of each category, integrated visualisation as well as additional tools have been developed.
Integrated visualisationOctopus is a visualisation tool that highlights correlations between entities of the database. From the Sept.2020 release, the interface described in the GlyConnect article cited above, was substantially modified to improve user-friendliness. In contrast with the set of coloured buttons that access information from a range of viewpoints, Octopus exclusively searches GlyConnect from the glycan perspective. It is designed to offer an alternative to drawing glycan structures, which can be time-consuming especially for users with limited glycoscience background.
This short video shows how to start with Octopus. Further examples of use are shown from 01:04:00 in the video #2 mentioned above.
Compozitor queries GlyConnect to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database.
For more details on Compozitor, see Help button (?) on the Compozitor page. Further examples of use are shown in video #2 mentioned above, from 24:20mn, 57:45mn and 1:12:40, as well as in video #3 mentioned above, from 21:20mn and 39:35mn.
GlycoSiteAlign selectively aligns amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., "fucosylated") or specific, such as precise composition, and are proposed in a drop-down list.
This tool was designed upon observing that the similarity of glycan structures (shared properties) impacts on the regularity of site alignment.
An example of use is shown from minute 15:37 in the video #4.
Glydin’ (Glycan dynamics) is 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. It was designed to (1) merge distinct sources of information and standardise the description glycoepitopes provided in different formats and (2) map the similarity between these entities in an interactive network.
An example of use is shown in this video.
Cross-references, controlled vocabularies and ontologies used in GlyConnect are detailed in this table:
| Category | Resource | URL |
| Glycan | GlyTouCan | glytoucan.org |
| Protein |
|
|
| Gene | GeneCards | genecards.org |
| 3D Structures | Protein Data Bank (via Litemol) | ebi.ac.uk/pdbe/ |
| Reference |
|
|
| Taxonomy | NCBI Taxonomy | ncbi.nlm.nih.gov/taxonomy |
| Tissue | Uberon ontology | uberon.org |
| Plant Tissue | BRENDA ontology | brenda-enzymes.org/ontology.php?ontology_id=3 |
| Cell Type | Cell ontology | cellontology.org |
| Cell Component | Gene ontology | geneontology.org |
| Cell line | Cellosaurus DB | web.expasy.org/cellosaurus |
| Disease | Disease Ontology | disease-ontology.org |
| Peptide variant | dbSNP | ncbi.nlm.nih.gov/projects/SNP |