Protein details/Glycosylation: Difference between revisions

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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.
The Glycosylation section of the [[Protein details]] page in GlyGen provides a detailed list of glycosylation sites, reported glycans attached to the protein, and sites text mined from publications.


==Glycosylation==
==Glycosylation==
[[File:Protein_Glycosylation_Screenshot.jpg|thumb|upright|Screenshot of the Glycosylation section on the [[Protein information]] page in GlyGen.]]
[[File:Protein_Glycosylation_Screenshot.jpg|thumb|upright|Screenshot of the Glycosylation section on the [[Protein details]] page in GlyGen.]]
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)
Glycosylation is presented in 4 tabs on the [[Protein details]] 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===
===Reported Sites with Glycan===
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This tab shows reported glycosylation sites without glycan information. The following columns are presented in the table:
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
*'''Source''' - GlyGen evidence linking to the databases and papers that provided the glycosylation information
* '''Type''' - Type of glycosylation. Eg. N-linked, O-linked
*'''Type''' - Type of glycosylation. Eg. N-linked, O-linked
* '''Residue''' - Amino acid residue of the given protein along with its position. Eg. Asn294
*'''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.


=== Predicted Only ===
===Predicted Only===
This tab shows predicted glycosylation sites. The following columns are presented in the table:
This tab shows predicted glycosylation sites. The following columns are presented in the table:


=== Text Mining ===
{{Expand section|small=no}}
 
===Text Mining===
{{Expand section|small=no}}
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==Source of information==
==Source of information==
{{Expand section|small=no}}
The Glycosylation data is collected and integrated from the resources such as '''[https://www.uniprot.org/ UniProtKB]''', [https://glyconnect.expasy.org/ '''Glyconnect'''], '''[http://www.unicarbkb.org/ UniCarbKB], [https://www.rcsb.org/ RCSB PDB], [https://www.oglcnac.mcw.edu/ The O-GlcNAc Database]'''.
The Glycosylation data is collected and integrated from the resources such as '''[https://www.uniprot.org/ UniProtKB]''', [https://glyconnect.expasy.org/ '''Glyconnect'''], '''[http://www.unicarbkb.org/ UniCarbKB], [https://www.rcsb.org/ RCSB PDB], [https://www.oglcnac.mcw.edu/ The O-GlcNAc Database]'''.


*[https://www.uniprot.org/ UniProtKB] - only reported sites information and predicted information is downloaded from UniProtKB
*[https://www.uniprot.org/ '''UniProtKB'''] - only reported sites information and predicted information is downloaded from UniProtKB
*[https://glyconnect.expasy.org/ Glyconnect] - reported sites with glycan information on known and unknown residues is downloaded from Glyconnect
*[https://glyconnect.expasy.org/ '''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
*'''[http://unicarbkb.org/ UniCarbKB]''' - reported sites with glycan information on known and unknown residues is downloaded from UniCarbKB
*[https://www.rcsb.org/ RCSB PDB] - only reported sites information is downloaded from RCSB PDB
*[https://www.rcsb.org/ '''RCSB PDB'''] - only reported sites information is downloaded from RCSB PDB
*[https://www.oglcnac.mcw.edu/ The O-GlcNAc Database] - Only O-GlcNAcylation reported sites with glycan information on known and unknown residues is downloaded from The O-GlcNAc database
*[https://www.oglcnac.mcw.edu/ '''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==
==Data access==
{{Expand section|small=no}}
The collected data is processed and stored in '''[https://data.glygen.org data.glygen.org]''' in the following datasets.
The collected data is processed and stored in '''[https://data.glygen.org data.glygen.org]''' in following datasets.


Homo Sapiens (Human) Datasets
Homo Sapiens (Human) Datasets

Latest revision as of 20:16, 19 May 2022

The Glycosylation section of the Protein details page in GlyGen provides a detailed list of glycosylation sites, reported glycans attached to the protein, and sites text mined from publications.

Glycosylation

Screenshot of the Glycosylation section on the Protein details page in GlyGen.

Glycosylation is presented in 4 tabs on the Protein details 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

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

The collected data is processed and stored in data.glygen.org in the 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

Data filtering

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