Protein details/Glycosylation: Difference between revisions
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===Reported Sites with Glycan=== | ===Reported Sites with Glycan=== | ||
This tab shows reported glycosylation sites with glycan information. The following columns are presented in the table: | |||
This tab shows | |||
*'''Source''' - GlyGen evidence linking to the databases and papers that provided the glycosylation information | *'''Source''' - GlyGen evidence linking to the databases and papers that provided the glycosylation information | ||
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*'''GlyTouCan ID''' - Unique accession assigned to the registered glycan structure in [https://glytoucan.org/ GlyTouCan] database. Eg. G01543ZX | *'''GlyTouCan ID''' - Unique accession assigned to the registered glycan structure in [https://glytoucan.org/ GlyTouCan] database. Eg. G01543ZX | ||
*'''Glycan Image''' - Image of the glycan in SNFG format | *'''Glycan Image''' - Image of the glycan in SNFG format | ||
*'''Residue''' - Amino acid residue of the given protein along with its position. | *'''Residue''' - Amino acid residue of the given protein along with its position. Eg. Asn294 | ||
*'''Note''' - Additional information about the entry such as curation notes, O-glycosylation subtype, remarks, etc. | *'''Note''' - Additional information about the entry such as curation notes, O-glycosylation subtype, remarks, etc. | ||
===Reported Sites=== | ===Reported Sites=== | ||
This tab shows reported glycosylation sites without glycan information. The following columns are presented in the table: | |||
* '''Source''' - GlyGen evidence linking to the databases and papers that provided the glycosylation information | |||
* '''Type''' - Type of glycosylation. Eg. N-linked, O-linked | |||
* '''Residue''' - Amino acid residue of the given protein along with its position. Eg. Asn294 | |||
* '''Note''' - Additional information about the entry such as curation notes, O-glycosylation subtype, remarks, etc. | |||
=== Predicted Only === | |||
This tab shows predicted glycosylation sites. The following columns are presented in the table: | |||
=== Text Mining === | |||
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==Source of information== | ==Source of information== | ||
{{Expand section|small=no}} | {{Expand section|small=no}} | ||
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Homo Sapiens (Human) Datasets | Homo Sapiens (Human) Datasets | ||
* Human Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000038 GLY_000038]) | *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]) | *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 (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 (GlyConnect; [https://data.glygen.org/GLY_000329 GLY_000329]) | ||
* Human Glycosylation Sites ([GPTwiki]; [https://data.glygen.org/GLY_000480 GLY_000480]) | *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 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 O-GlcNAc Glycosylation Sites (MCW; [https://data.glygen.org/GLY_000517 GLY_000517]) | ||
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Hepatitis C Virus Datasets | Hepatitis C Virus Datasets | ||
* HCV1a Glycosylation Sites (Literature + UniCarbKB; [https://data.glygen.org/GLY_000335 GLY_000335]) | *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]) | *HCV1a Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000382 GLY_000382]) | ||
*HCV1b Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000383 GLY_000383]) | *HCV1b Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000383 GLY_000383]) | ||
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SARS Coronavirus Datasets | SARS Coronavirus Datasets | ||
* SARS-CoV2 Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000473 GLY_000473]) | *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]) | *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-CoV1 Glycosylation Sites (UniProtKB; [https://data.glygen.org/GLY_000495 GLY_000495]) |
Revision as of 16:00, 23 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
This tab shows reported glycosylation sites with glycan information. The following columns are presented in the table:
- 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. Eg. Asn294
- Note - Additional information about the entry such as curation notes, O-glycosylation subtype, remarks, etc.
Reported Sites
This tab shows reported glycosylation sites without glycan information. The following columns are presented in the table:
- Source - GlyGen evidence linking to the databases and papers that provided the glycosylation information
- Type - Type of glycosylation. Eg. N-linked, O-linked
- Residue - Amino acid residue of the given protein along with its position. Eg. Asn294
- Note - Additional information about the entry such as curation notes, O-glycosylation subtype, remarks, etc.
Predicted Only
This tab shows predicted glycosylation sites. The following columns are presented in the table:
Text Mining
Source of information
This section needs expansion. You can help by adding to it. |
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
This section needs expansion. You can help by adding to it. |
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
This section needs expansion. You can help by adding to it. |
Data filtering
This section needs expansion. You can help by adding to it. |