HGNC gene links to GtoPdb

As regular users of GtoPdb will be aware, our target pages include HUGO Gene Nomenclature Committee (HGNC) gene symbols, nomenclature and links to HGNC gene pages (Fig 1).

gene_link_screenshot

Figure 1. GtoPdb gene information including link outs to HGNC pages by clicking on the human gene symbol.

HGNC pages in turn link back to GtoPdb target pages under the “Specialist database” link (Fig 2).

hgnc_target_link

Figure 2. HGNC gene page showing the link to the IUPHAR/BPS Guide to Pharmacology (GtoPdb) under “Specialist Databases”.

In GtoPdb release 2017.4 there were 2823 HGNC target links. In June 2017 we also added a further 430 HGNC links to GtoPdb peptide ligand pages (Figs 3 and 4). These are either small proteins such as cytokines, or endogenous peptides derived from Swiss-Prot proteins that have an HGNC entry. Implicit in our classification as ligands these will have (in most cases quantitative) reported interactions with cognate receptors.  The peptides will usually correspond to sequences processed from their precursor proteins in HGNC (e.g. the eight angiotensin peptides from Angiotensinogen, AGT).  Note that some of these peptides are cross-linked to other ligand entries which are similar synthetic bioactive sequences that do not exactly match the cleavage cross-references in UniProt.

ligand_gene

Figure 3. GtoPdb peptide ligand page which links to the HGNC gene page by clicking on the gene symbol.

hgnc_ligand_link

Figure 4. HGNC gene page for a chemokine ligand showing a link to the GtoPdb ligand page.

For over 50 genes which encode multiple mature peptides, the HGNC page links to the longest peptide sequence included in GtoPdb. This is because HGNC currently only supports one external link per resource, and they are working on providing support for multiple links by the end of this year.

This expansion was driven by importance of these reciprocal links for HGNC users to navigate across to pharmacolgical information. In addtion, going the other way, they enable GtoPdb users to find out more about gene nomenclature and other genetic information via HGNC.

The full list of HGNC in-links to GtoPdb can be downloaded here (as a CSV file as illustrated in Fig 5). Ligand links can be distinguished from target links by the URL.

genes

Figure 5. Part of the CSV file containing all the HGNC links to GtoPdb showing some of the new ligand links.

 

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