Protein details/Names: Difference between revisions

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The names section of the [[Protein information]] page in GlyGen provides information about the protein and gene name(s) and synonym(s).
The Names section of the [[Protein details]] page in GlyGen provides information about the protein and gene name(s) and synonym(s).


==Names==
==Names==
[[File:Protein Names Screenshot.png|thumb|Screenshot of the Names section on the [[Protein details]] page in GlyGen.]]
This section provides the following information:
This section provides the following information:


* '''Gene Name (recommended)''':  Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC), mouse gene names/symbols are approved by the Mouse Genome Informatics (MGI), whereas rat gene names and symbols are approved by Rat Genome Nomenclature Committee (RGNC). Eg. [https://www.uniprot.org/uniprot/P14210 HGF].
*'''Gene Name (Recommended)''':  Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC), mouse gene names/symbols are approved by the Mouse Genome Informatics (MGI), whereas rat gene names and symbols are approved by Rat Genome Nomenclature Committee (RGNC). Eg. HGF
* '''Gene Name (synonyms)''': Synonymous names for the given gene name, assigned by UniProtKB and RefSeq. Eg. UniProtKB: HPTA RefSeq: DFNB39; F-TCF; HGFB; HPTA; SF; HGF
*'''Gene Name (Synonyms)''': Synonymous names for the given gene name, assigned by UniProtKB and RefSeq. Eg. HPTA; DFNB39; F-TCF; HGFB; HPTA; SF; HGF
* '''Protein Name (recommended)''': Protein name assigned by UnitProtKB which follows international protein nomenclature guidelines. Eg. UniProtKB: [https://www.uniprot.org/uniprot/P14210#names_and_taxonomy Hepatocyte growth factor]
*'''Protein Name (Recommended)''': Protein name assigned by UnitProtKB which follows international protein nomenclature guidelines. Eg. Hepatocyte growth factor
* '''Protein Name (synonyms)''': Synonymous names for the given protein name, assigned by UniProtKB. Eg. UniProtKB: [https://www.uniprot.org/uniprot/P14210#names_and_taxonomy Hepatocyte growth factor isoform 6]
*'''Protein Name (Synonyms)''': Synonymous names for the given protein name, assigned by UniProtKB and NCBI RefSeq name with official nomenclature, when available. Eg. Hepatocyte growth factor isoform 6
* '''RefSeq:''' NCBI reference sequence name with official nomenclature when available.


==Source of information==
The Names data is collected and integrated from '''[https://uniprot.org UniProtKB]''' and '''[https://www.ncbi.nlm.nih.gov/ NCBI RefSeq]''' databases.
*[https://uniprot.org/ '''UniProtKB'''] - alternative names taken from UniProtKB protein accessions
*'''[https://www.ncbi.nlm.nih.gov/ NCBI RefSeq]''' - primary and other alternative/synonym protein names taken from the NCBI RefSeq database
==Data access==
The collected data is processed and stored at '''[https://data.glygen.org/ data.glygen.org]''' in the following datasets:
Homo Sapiens (Human) Datasets
*Human Protein Alternative Name (UniProtKB; [https://data.glygen.org/GLY_000031 GLY_000031])
*Human Protein Recommended Names (UniProtKB; [https://data.glygen.org/GLY_000087 GLY_000087])
*Human Gene Symbols (NCBI RefSeq; [https://data.glygen.org/GLY_000387 GLY_000387])
*Human Protein Names (NCBI RefSeq; [https://data.glygen.org/GLY_000392 GLY_000392])
*Human Protein Submitted Names (UniProtKB; [https://data.glygen.org/GLY_000395 GLY_000395])
*Human Gene Symbols (UniProtKB; [https://data.glygen.org/GLY_000401 GLY_000401])
Hepatitis C Virus Datasets


*HCV1a Protein Recommended Names (UniProtKB; [https://data.glygen.org/GLY_000357 GLY_000357])
*HCV1a Protein Alternative Name (UniProtKB; [https://data.glygen.org/GLY_000359 GLY_000359])
*HCV1b Protein Recommended Names (UniProtKB; [https://data.glygen.org/GLY_000358 GLY_000358])
*HCV1b Protein Alternative Name (UniProtKB; [https://data.glygen.org/GLY_000360 GLY_000360])


==Source of information==
SARS Coronavirus Datasets
 
*SARS-CoV1 Protein Alternative Name (UniProtKB; [https://data.glygen.org/GLY_000413 GLY_000413])
*SARS-CoV1 Gene Symbols (UniProtKB; [https://data.glygen.org/GLY_000425 GLY_000425])
*SARS-CoV1 Protein Names (NCBI RefSeq; [https://data.glygen.org/GLY_000437 GLY_000437])
*SARS-CoV1 Protein Recommended Names (UniProtKB; [https://data.glygen.org/GLY_000438 GLY_000438])
*SARS-CoV2 Protein Names (NCBI RefSeq; [https://data.glygen.org/GLY_000613 GLY_000613])
 
Mus musculus (Mouse) Datasets
 
*Mouse Protein Alternative Name (UniProtKB; [https://data.glygen.org/GLY_000032 GLY_000032])
*Mouse Protein Recommended Names (UniProtKB; [https://data.glygen.org/GLY_000088 GLY_000088])
*Mouse Gene Symbols (NCBI RefSeq; [https://data.glygen.org/GLY_000388 GLY_000388])
*Mouse Gene Symbols (UniProtKB; [https://data.glygen.org/GLY_000391 GLY_000391])
*Mouse Protein Names (NCBI RefSeq; [https://data.glygen.org/GLY_000393 GLY_000393])
*Mouse Protein Submitted Names (UniProtKB; [https://data.glygen.org/GLY_000396 GLY_000396])
 
Rattus norvegicus (Rat) Datasets


==Data access==
*Rat Protein Recommended Names (UniProtKB; [https://data.glygen.org/GLY_000222 GLY_000222])
*Rat Protein Alternative Name (UniProtKB; [https://data.glygen.org/GLY_000265 GLY_000265])
*Rat Gene Symbols (NCBI RefSeq; [https://data.glygen.org/GLY_000389 GLY_000389])
*Rat Gene Symbols (UniProtKB; [https://data.glygen.org/GLY_000390 GLY_000390])
*Rat Protein Names (NCBI RefSeq; [https://data.glygen.org/GLY_000394 GLY_000394])
*Rat Protein Submitted Names (UniProtKB; [https://data.glygen.org/GLY_000397 GLY_000397])


==Data harmonization==
==Data harmonization==
{{Expand section|small=no}}


==Data filtering==
==Data filtering==
{{Expand section|small=no}}

Latest revision as of 15:18, 9 December 2021

The Names section of the Protein details page in GlyGen provides information about the protein and gene name(s) and synonym(s).

Names

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

This section provides the following information:

  • Gene Name (Recommended): Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC), mouse gene names/symbols are approved by the Mouse Genome Informatics (MGI), whereas rat gene names and symbols are approved by Rat Genome Nomenclature Committee (RGNC). Eg. HGF
  • Gene Name (Synonyms): Synonymous names for the given gene name, assigned by UniProtKB and RefSeq. Eg. HPTA; DFNB39; F-TCF; HGFB; HPTA; SF; HGF
  • Protein Name (Recommended): Protein name assigned by UnitProtKB which follows international protein nomenclature guidelines. Eg. Hepatocyte growth factor
  • Protein Name (Synonyms): Synonymous names for the given protein name, assigned by UniProtKB and NCBI RefSeq name with official nomenclature, when available. Eg. Hepatocyte growth factor isoform 6

Source of information

The Names data is collected and integrated from UniProtKB and NCBI RefSeq databases.

  • UniProtKB - alternative names taken from UniProtKB protein accessions
  • NCBI RefSeq - primary and other alternative/synonym protein names taken from the NCBI RefSeq database

Data access

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

Homo Sapiens (Human) Datasets

Hepatitis C Virus Datasets

  • HCV1a Protein Recommended Names (UniProtKB; GLY_000357)
  • HCV1a Protein Alternative Name (UniProtKB; GLY_000359)
  • HCV1b Protein Recommended Names (UniProtKB; GLY_000358)
  • HCV1b Protein Alternative Name (UniProtKB; GLY_000360)

SARS Coronavirus Datasets

  • SARS-CoV1 Protein Alternative Name (UniProtKB; GLY_000413)
  • SARS-CoV1 Gene Symbols (UniProtKB; GLY_000425)
  • SARS-CoV1 Protein Names (NCBI RefSeq; GLY_000437)
  • SARS-CoV1 Protein Recommended Names (UniProtKB; GLY_000438)
  • SARS-CoV2 Protein Names (NCBI RefSeq; GLY_000613)

Mus musculus (Mouse) Datasets

Rattus norvegicus (Rat) Datasets

Data harmonization

Data filtering

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