Protein details/Glycosylation: Difference between revisions
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The collected data is processed and stored in '''[https://data.glygen.org data.glygen.org]''' in following datasets. | The collected data is processed and stored in '''[https://data.glygen.org data.glygen.org]''' in following datasets. | ||
Homo Sapiens Datasets | Homo Sapiens (Human) Datasets | ||
* Human Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000038 GLY_000038]) | |||
* Glycosylation Sites (UniCarbKB [Human proteins]; [https://data.glygen.org/GLY_000040 GLY_000040]) | |||
* Human Glycosylation Sites (RCSB PDB; [https://data.glygen.org/GLY_000042 GLY_000042]) | |||
* Human Glycosylation Sites (GlyConnect; [https://data.glygen.org/GLY_000329 GLY_000329]) | |||
* Human Glycosylation Sites ([GPTwiki]; [https://data.glygen.org/GLY_000480 GLY_000480]) | |||
*Human Glycosylation Sites ([Automatic Literature Mining] [Automatically verified]; [https://data.glygen.org/GLY_000481 GLY_000481]) | |||
*Human O-GlcNAc Glycosylation Sites (MCW; [https://data.glygen.org/GLY_000517 GLY_000517]) | |||
*Human Glycosylation Sites UniCarbKB Glycomics Study ([https://data.glygen.org/GLY_000611 GLY_000611]) | |||
Hepatitis C Virus Datasets | Hepatitis C Virus Datasets | ||
* HCV1a Glycosylation Sites (Literature + UniCarbKB; [https://data.glygen.org/GLY_000335 GLY_000335]) | |||
*HCV1a Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000382 GLY_000382]) | |||
*HCV1b Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000383 GLY_000383]) | |||
SARS Coronavirus Datasets | SARS Coronavirus Datasets | ||
* SARS-CoV2 Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000473 GLY_000473]) | |||
*Glycosylation Sites (UniCarbKB [SARS CoV 2 proteins]; [https://data.glygen.org/GLY_000479 GLY_000479]) | |||
*SARS-CoV1 Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000495 GLY_000495]) | |||
*SARS-CoV2 Glycosylation sites (UniprotKB; [https://data.glygen.org/GLY_000473 GLY_000473]) | |||
*SARS-CoV1 Glycosylation Sites (Literature; [https://data.glygen.org/GLY_000612 GLY_000612]) | |||
Mus musculus (Mouse) Datasets | |||
*Mouse Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000039 GLY_000039]) | *Mouse Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000039 GLY_000039]) | ||
*Glycosylation sites (UniCarbKB [Mouse proteins]; [https://data.glygen.org/GLY_000041 GLY_000041]) | *Glycosylation sites (UniCarbKB [Mouse proteins]; [https://data.glygen.org/GLY_000041 GLY_000041]) | ||
*Mouse Glycosylation Sites (RCSB PDB; [https://data.glygen.org/GLY_000043 GLY_000043]) | *Mouse Glycosylation Sites (RCSB PDB; [https://data.glygen.org/GLY_000043 GLY_000043]) | ||
*Mouse Glycosylation Sites (GlyConnect; [https://data.glygen.org/GLY_000330 GLY_000330]) | |||
Rattus norvegicus (Rat) Datasets | |||
*Glycosylation sites (UniCarbKB [Rat proteins]; [https://data.glygen.org/GLY_000221 GLY_000221]) | *Glycosylation sites (UniCarbKB [Rat proteins]; [https://data.glygen.org/GLY_000221 GLY_000221]) | ||
*Rat Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000224 GLY_000224]) | *Rat Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000224 GLY_000224]) | ||
*Rat Glycosylation Sites (RCSB PDB; [https://data.glygen.org/GLY_000226 GLY_000226]) | *Rat Glycosylation Sites (RCSB PDB; [https://data.glygen.org/GLY_000226 GLY_000226]) | ||
*Rat Glycosylation Sites (GlyConnect; [https://data.glygen.org/GLY_000331 GLY_000331]) | *Rat Glycosylation Sites (GlyConnect; [https://data.glygen.org/GLY_000331 GLY_000331]) | ||
==Data harmonization== | ==Data harmonization== |
Revision as of 21:22, 11 November 2021
The glycosylation section of the Protein information page in GlyGen provides the detailed list of glycosylation sites, reported glycans attached to the protein and predicted sites.
Glycosylation
![](/images/thumb/a/ae/Protein_Glycosylation_Screenshot.jpg/230px-Protein_Glycosylation_Screenshot.jpg)
Glycosylation is presented in 4 tabs on the Protein information page in GlyGen. The Glycosylation summary provides the overall information about the section like the total number of sites (O,N,S,C linked sites), total number of N linked and O-linked sites with the total number of glycan annotations (structures) observed on the protein. Eg. 18 site(s) total, 169 N-linked annotation(s) at 17 site(s), 1 O-linked annotation(s) at 1 site(s)
Reported Sites with Glycan
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This tab shows a table with the following columns:
- Source - GlyGen evidence linking to the databases and papers that provided the glycosylation information
- Type - Type of glycosylation. Eg. N-linked, O-linked
- GlyTouCan ID - Unique accession assigned to the registered glycan structure in GlyTouCan database. Eg. G01543ZX
- Glycan Image - Image of the glycan in SNFG format
- Residue - Amino acid residue of the given protein along with its position.
- Note - Additional information about the entry such as curation notes, O-glycosylation subtype, remarks, etc.
Reported Sites
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Source of information
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The Glycosylation data is collected and integrated from the resources such as UniProtKB, Glyconnect, UniCarbKB, RCSB PDB, The O-GlcNAc Database.
- UniProtKB - only reported sites information and predicted information is downloaded from UniProtKB
- Glyconnect - reported sites with glycan information on known and unknown residues is downloaded from Glyconnect
- UniCarbKB - reported sites with glycan information on known and unknown residues is downloaded from UniCarbKB
- RCSB PDB - only reported sites information is downloaded from RCSB PDB
- The O-GlcNAc Database - Only O-GlcNAcylation reported sites with glycan information on known and unknown residues is downloaded from The O-GlcNAc database
Data access
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The collected data is processed and stored in data.glygen.org in following datasets.
Homo Sapiens (Human) Datasets
- Human Glycosylation Sites (UniProtKB; GLY_000038)
- Glycosylation Sites (UniCarbKB [Human proteins]; GLY_000040)
- Human Glycosylation Sites (RCSB PDB; GLY_000042)
- Human Glycosylation Sites (GlyConnect; GLY_000329)
- Human Glycosylation Sites ([GPTwiki]; GLY_000480)
- Human Glycosylation Sites ([Automatic Literature Mining] [Automatically verified]; GLY_000481)
- Human O-GlcNAc Glycosylation Sites (MCW; GLY_000517)
- Human Glycosylation Sites UniCarbKB Glycomics Study (GLY_000611)
Hepatitis C Virus Datasets
- HCV1a Glycosylation Sites (Literature + UniCarbKB; GLY_000335)
- HCV1a Glycosylation Sites (UniProtKB; GLY_000382)
- HCV1b Glycosylation Sites (UniProtKB; GLY_000383)
SARS Coronavirus Datasets
- SARS-CoV2 Glycosylation Sites (UniProtKB; GLY_000473)
- Glycosylation Sites (UniCarbKB [SARS CoV 2 proteins]; GLY_000479)
- SARS-CoV1 Glycosylation Sites (UniProtKB; GLY_000495)
- SARS-CoV2 Glycosylation sites (UniprotKB; GLY_000473)
- SARS-CoV1 Glycosylation Sites (Literature; GLY_000612)
Mus musculus (Mouse) Datasets
- Mouse Glycosylation Sites (UniProtKB; GLY_000039)
- Glycosylation sites (UniCarbKB [Mouse proteins]; GLY_000041)
- Mouse Glycosylation Sites (RCSB PDB; GLY_000043)
- Mouse Glycosylation Sites (GlyConnect; GLY_000330)
Rattus norvegicus (Rat) Datasets
- Glycosylation sites (UniCarbKB [Rat proteins]; GLY_000221)
- Rat Glycosylation Sites (UniProtKB; GLY_000224)
- Rat Glycosylation Sites (RCSB PDB; GLY_000226)
- Rat Glycosylation Sites (GlyConnect; GLY_000331)
Data harmonization
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Data filtering
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