Demo

GlyGen demo registration

No Upcoming demo

Last demo

2021-04-06

GlyGen features: Super Search; GlyGen ID mapping; Protein site search (glycosylation site, mutation).

Recording: https://www.youtube.com/watch?v=Xw9AECStmQI

Questions from GlyGen Demo April 06, 2021

Q) Do you plan to integrate some tools that can also build the 3D structure of glycans? For example, Glycam sequences that can be used to model structure in Glycam web?

A) Yes, GlyGen is working with GLYCAM resource to generate 3D structures for glycan and glycoproteins using the GLYCAM 3D structure visualizer and  builder. The generated 3D structures will be made available to users in coming months.

Q) Thanks for the overview.  I'm just getting familiar with GlyGen.  Can you elaborate on utility for proteoglycans? (question will be shortened)

A) GlyGen does not currently support proteoglycan glycan-protein conjugates, though some of the typical proteoglycan GAG glycans are present in GlyGen as glycan entries. We are currently working to support the classification of GAG glycans in the GlycoMotif and GlycanData projects to make these glycans easier to find. Our current support for glycan-protein conjugates (data-model, web-site) is focused on glycoproteins.

Q) The tools you showed can be used with proteoglycans and glycosaminoglycans?

What organisms do you plan to include in future updates?

A) See answer above, some GAGs are present, though the repeating structure definitions are not generally well supported by our glycan structure analysis tools. Where these GlyTouCan accessions have annotations, these are captured and presented just as any others are. We have planned to add Drosophila as our next organisms. We are also evaluating other model organisms, pathogenic microbes and viruses.

Q) Will GlyGen have its own curation of glycoenzymes to glycosylation pathways (N-linked, O-linked GSL GAG), or will this information be cross referenced from other databases? Thank you!

A) GlyGen has been curating and maintaining a set of glycoenzymes (glycosyltransferases and glycohydrolases) for human, mouse and rat organisms. Eg - Here is a list of Human Glycosyltransferases - https://data.glygen.org/GLY_000004. Whereas the information for glycosylation pathways for such glycoenzymes is being integrated from resources such as Reactome, Rhea, KEGG etc.) From the available knowledge and expertise, GlyGen has been developing an interactive tool ‘Sandbox’ that will allow users to explore glycan biosynthetic pathways. Check out the current version of Sandbox - https://glygen.ccrc.uga.edu/sandbox/

Q) What are your upcoming plans for new tools?

A) In the coming months, we plan to develop tools such as glycan drawing and naming tool to draw and search glycans, batch retrieval tool that will allow batch retrieval of glycans and proteins, BLAST to search for glycopeptides and glycoproteins, basket tool to add selected glycans and proteins for further exploration, advanced composition search tool with more options to search for glycan compositions, (glycan sequence converter?) etc. We also plan to add more functionalities and enhance the existing developed tools.

Q) Can the DB be used to investigate the use of GP as adjuvants?

Q) Are there functions to filter glycans with exact structures?  Some structures have ambiguous structure.

A) The GlyGen’s Super Search option can be used to filter fully defined/determined glycans. In the Super Search, select Glycan property and select fully defined option and search to get a list of fully defined glycans. Alternatively, you can access the dataset that contains fully defined/determined structures in GlyGen (https://data.glygen.org/GLY_000326). We are also working on a feature to filter glycans from list pages of other glycan searches with fully determined structures and will be available in the next GlyGen release.

Q) Are you planning to expand the data for fungi and bacteria?

A) We are exploring the possibility of integrating the data for plants, fungi and bacteria but given the complexity involved in the integration (selection of proteome, data model) such integration will be evaluated and planned in the future.

Q) Thanks for the demo, I'm sure more questions will come up once people start using GlyGen. Does it also include mucin type O-glycans? And what about microbial glycosylation? Is this something you are looking to expand to in the future? (Question will be shortened)

A) GlyGen does include mucin type O-glycans and can be searched and explored through the glycan advanced search page by selecting Glycan type as O-linked and then by selecting the appropriate Glycan subtype. Alternatively, you can perform the search through Super Search by selecting the option O-linked from Glycan class and choose the appropriate subclass from the Glycan subclass option. See above answer regarding bacterial glycans.

Q) When searching  for proteins or sites that have a particular glycan, how restrictive are the requirements for linkage isomers? Does searching for a specific linkage for a fucose or sialic acid include results with unknown linkage, or does the search only return glycans with those specific linkages?

A) The association between a protein site and glycan is represented by the GlyGen/GlyTouCan accession of the glycan that precisely captures the known and unknown status of each linkage. However, the GNOme Structure Browser applet (called Related Glycans on Glycan pages) make it possible to explore related glycan accessions by subsumption, and/or to place all subsuming (ancestor accessions) or subsumed (descendant accession) in the copy-and-paste clipboard. These accessions can be used with the Advanced Glycan Search. Some GlyGen data-types and searches are subsumption-aware and will apply this logic automatically, though support for this is still preliminary.

Q) What are the advantages of the GlyGen server in comparison to the other glycan/carbohydrate databases, e.g., GlyTouCan?

A) GlyTouCan (https://glytoucan.org/) is a resource for registering glycans and a repository for storing glycans structures, similar to NCBI GenBank that is a repository for nucleotide sequences. Whereas resources like GlyGen are data dissemination knowledgebases that integrate diverse types of data from multiple data sources  and harmonize this data for further exploration. GlyGen not only contain knowledge about glycans but it also contains extensive knowledge about genes, glycoproteins, glycoenzymes. GlyGen collaborates with GlyTouCan to harmonize data.

Q) Are all the glycan information in GlyGen based on the published results?

A) Not all glycans integrated in GlyGen have literature evidence associated with it. Although, for most glycans that can be seen from a protein entry have literature evidence. The publication section on Glycan detail pages lists the literature evidence when available. Most glycan information, especially the information supplied by third-party data-providers, is evidence tagged with the source of the information. Some of these data-providers provide their annotations on the basis of publications and include information about the publication with their annotations, these are displayed as badges alongside the data-provider badges.