Protein details/Phosphorylation: Difference between revisions

Latest revision as of 17:39, 9 December 2021

The Phosphorylation section of the Protein details page in GlyGen provides a detailed list of phosphorylation sites and kinase proteins responsible for phosphorylation.

Phosphorylation

This section provides the following information:

Source - Evidence linking to the databases and papers that provided the phosphorylation information.
Kinase Protein - GlyGen ID of the enzyme responsible for catalyzing the covalent addition of a phosphate group to the protein. Eg. Q6P1J9-1
Kinase Gene - Name of the gene that encodes the kinase protein. Eg. CDC73
Residue - Residue on which phosphorylation occurs by kinase protein; commonly occurs on amino acids serine and threonine, and occasionally tyrosine. Eg. Ser322
Notes - Additional information about the entry such as curation notes, phosphorylation subtype, remarks, etc.

Source of information

The Phosphorylation data is collected and integrated from UniProtKB, PubMed, and iPTMnet databases.

UniProtKB - only reported sites information and predicted information is downloaded from UniProtKB.
iPTMnet - only reported sites information and predicted information is downloaded from iPTMnet

Data access

The collected data is processed and stored in data.glygen.org in following datasets.

Homo Sapiens (Human) Datasets

Human Phosphorylation Sites (UniProtKB; GLY_000274)
Human Phosphorylation Sites (iPTMNet; GLY_000519)

Hepatitis C Virus Datasets

HCV1a Phosphorylation Sites (UniProtKB; GLY_000384)
HCV1b Phosphorylation Sites (UniProtKB; GLY_000385)

SARS Coronavirus Datasets

SARS-CoV1 Phosphorylation Sites (UniProtKB; GLY_000474)
SARS-CoV2 Phosphorylation Sites (UniProtKB; GLY_000475)

Mus musculus (Mouse) Datasets

Mouse Phosphorylation Sites (UniProtKB; GLY_000254)
Mouse Phosphorylation Sites (iPTMNet; GLY_000520)

Rattus norvegicus (Rat) Datasets

Rat Phosphorylation Sites (UniProtKB; GLY_000231)
Rat Phosphorylation Sites (iPTMnet; GLY_000521)

Data harmonization

Data filtering

@@ Line 1: / Line 1: @@
-The Phosphorylation section of the [[Protein information]] page in GlyGen provides the detailed list of phosphorylation sites and kinase proteins responsible for phosphorylation.
+The Phosphorylation section of the [[Protein details]] page in GlyGen provides a detailed list of phosphorylation sites and kinase proteins responsible for phosphorylation.
 ==Phosphorylation==
-[[File:Protein Phosphorylation Screenshot.png|thumb|Screenshot of the Phosphorylation section on the [[Protein information]] page in GlyGen.]]
+[[File:Protein Phosphorylation Screenshot.png|thumb|Screenshot of the Phosphorylation section on the [[Protein details]] page in GlyGen.]]
 This section provides the following information:
-*'''Source''' -
+*'''Source''' - Evidence linking to the databases and papers that provided the phosphorylation information.
-*'''Kinase Protein''' -
+*'''Kinase Protein''' - GlyGen ID of the enzyme responsible for catalyzing the covalent addition of a phosphate group to the protein. Eg. Q6P1J9-1
-*'''Kinase Gene''' -
+*'''Kinase Gene''' - Name of the gene that encodes the kinase protein. Eg. CDC73
-*'''Residue''' -
+*'''Residue''' - Residue on which phosphorylation occurs by kinase protein; commonly occurs on amino acids serine and threonine, and occasionally tyrosine. Eg. Ser322
-*'''Notes''' -
+*'''Notes''' - Additional information about the entry such as curation notes, phosphorylation subtype, remarks, etc.
 ==Source of information==
 The Phosphorylation data is collected and integrated from '''[https://uniprot.org UniProtKB]''', '''[https://pubmed.ncbi.nlm.nih.gov/ PubMed]''', and '''[https://research.bioinformatics.udel.edu/iptmnet/ iPTMnet]''' databases.
+*'''[https://www.uniprot.org/ UniProtKB]''' - only reported sites information and predicted information is downloaded from UniProtKB.
+*'''[https://research.bioinformatics.udel.edu/iptmnet/ iPTMnet]''' - only reported sites information and predicted information is downloaded from iPTMnet
+{{Expand section|small=no}}
 ==Data access==
@@ Line 19: / Line 23: @@
 Homo Sapiens (Human) Datasets
-* Human Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000274 GLY_000274])
+*Human Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000274 GLY_000274])
-* Human Phosphorylation Sites (iPTMNet; [https://data.glygen.org/GLY_000519 GLY_000519])
+*Human Phosphorylation Sites (iPTMNet; [https://data.glygen.org/GLY_000519 GLY_000519])
 Hepatitis C Virus Datasets
+*HCV1a Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000384 GLY_000384])
+*HCV1b Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000385 GLY_000385])
+SARS Coronavirus Datasets
+*SARS-CoV1 Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000474 GLY_000474])
+*SARS-CoV2 Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000475 GLY_000475])
+Mus musculus (Mouse) Datasets
+*Mouse Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000254 GLY_000254])
+*Mouse Phosphorylation Sites (iPTMNet; [https://data.glygen.org/GLY_000520 GLY_000520])
+Rattus norvegicus (Rat) Datasets
+*Rat Phosphorylation Sites (UniProtKB; [https://data.glygen.org/GLY_000231 GLY_000231])
+*Rat Phosphorylation Sites (iPTMnet; [https://data.glygen.org/GLY_000521 GLY_000521])
 *
 ==Data harmonization==
+{{Expand section|small=no}}
 ==Data filtering==
+{{Expand section|small=no}}
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