Template:Infobox gene

Infobox Gene documentationviewedithistorypurge

This is the Infobox gene template. The data in the infobox is sourced from Wikidata. The Lua implementation of this template is located at Module:Infobox gene.

Usage on a gene page

Add {{infobox gene}} to the top of a gene page. The infobox is populated via the Wikidata item of the page it resides on. To view which Wikidata item is linked to a page, follow the "Wikidata items" link from the "Tools" menu to the left of the article.

Usage on a protein page

Add {{infobox gene}} to the top of a protein page. The infobox is populated by using the Wikidata item of the protein to find the encoded gene item and then uses the gene item to populate the infobox.

Usage on other pages

Any page can display the infobox even if it does not have a gene or protein interwiki link. The Wikidata item must be explicitly added as a parameter and the underlying module is invoked. For instance, appending {{#invoke:Infobox_gene|getTemplateData|QID=Q414043}} to the top of any page will create an infobox for the gene RELN. QID is the Wikidata gene item used to populate the infobox. Substitute the wikidata item id (QID) of interest as the QID parameter.

Error message

"An Error has occurred retrieving Wikidata item for infobox" Indicates a non gene/protein Wikidata item or an incomplete Wikidata item.

Categories

Including this template will automatically result in the addition of relevant categories based on the properties of the gene. These include Category:Human proteins and categories that correspond to the chromosome where the gene is located, such as Category:Genes on human chromosome 19. Other categories added manually to the article apart from the template will work as usual.

Parameters

RELN
Human reelin structure
Identifiers
Aliases	RELN, LIS2, PRO1598, RL, reelin, ETL7
External IDs	OMIM: 600514; MGI: 103022; GeneCards: RELN
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2ddu, 2e26, 2DDU, 2E26, 3A7Q
Gene location (Human) Chr. Chromosome 7 (human) Band 7q22.1 Start 103,471,381 bp End 103,989,658 bp
Gene location (Mouse) Chr. Chromosome 5 (mouse) Band 5 A3|5 9.98 cM Start 22,089,452 bp End 22,549,700 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in olfactory bulb cerebellar vermis cerebellar hemisphere paraflocculus of cerebellum right hemisphere of cerebellum spinal ganglia trigeminal ganglion endothelial cell tibial nerve pons Top expressed in ciliary body cerebellar vermis lobe of cerebellum iris olfactory bulb sciatic nerve endothelial cell of lymphatic vessel superior colliculus paraventricular nucleus of hypothalamus piriform cortex More reference expression data BioGPS More reference expression data
Gene ontology Molecular function metal ion binding peptidase activity hydrolase activity serine-type peptidase activity lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding Cellular component cytoplasm dendrite plasma membrane extracellular region extracellular space membrane extracellular matrix neuron projection Biological process NMDA glutamate receptor clustering positive regulation of lateral motor column neuron migration dendrite development proteolysis cerebral cortex development lateral motor column neuron migration positive regulation of phosphatidylinositol 3-kinase signaling positive regulation of TOR signaling long-term memory multicellular organism development receptor localization to synapse postsynaptic density protein 95 clustering ventral spinal cord development protein localization to synapse forebrain development long-term potentiation regulation of gene expression layer formation in cerebral cortex cell migration learning associative learning cell adhesion hippocampus development spinal cord patterning cerebral cortex tangential migration positive regulation of peptidyl-tyrosine phosphorylation glial cell differentiation peptidyl-tyrosine phosphorylation positive regulation of excitatory postsynaptic potential positive regulation of CREB transcription factor activity positive regulation of protein kinase activity modulation of chemical synaptic transmission positive regulation of AMPA receptor activity brain development central nervous system development response to pain positive regulation of synapse maturation positive regulation of long-term synaptic potentiation cell morphogenesis involved in differentiation neuron migration positive regulation of neuron projection development positive regulation of small GTPase mediated signal transduction positive regulation of synaptic transmission, glutamatergic regulation of behavior positive regulation of dendritic spine morphogenesis reelin-mediated signaling pathway regulation of NMDA receptor activity positive regulation of protein tyrosine kinase activity axon guidance Sources:Amigo / QuickGO
Orthologs Databases NCBI: entry; OMA: entry Species Human Mouse Entrez 5649 19699 Ensembl ENSG00000189056 ENSMUSG00000042453 UniProt P78509 Q60841 RefSeq (mRNA) NM_173054 NM_005045 NM_011261 NM_001310464 RefSeq (protein) NP_005036 NP_774959 NP_001297393 NP_035391 Location (UCSC) Chr 7: 103.47 – 103.99 Mb Chr 5: 22.09 – 22.55 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

Infobox gene is automatic but does have two parameters:

• QID : Changes the transcluded wikidata item. Example: {{infobox gene|QID=Q414043}}
• collapse_orthologs: Collapses the bottom section automatically upon opening a page, useful to make space on pages with lots of thumbnail images. Example: (currently only reliably working with #invoke) {{#invoke:Infobox_gene|getTemplateData|collapse_orthologs=1}} Collapsed form shown to the right.

Data structure

Basic network structure of the ProteinBoxBot wikidata project

Data structure of gene and protein data in Wikidata is a bit complex. Even if there is only one gene/protein article in Wikipedia, there are many data pages in Wikidata.

Basically Wikidata has distinct pages for gene and protein each, for respective species (See the table below). And pages are interconnected based on following rules.

• Wikipedia articles are connected to Wikidata's gene data page (#Case A) or protein data page (#Case B) through d:Help:Sitelinks. In most cases, articles are connected to gene data page.
• Gene and protein pages are interconnected through "encodes (d:P:P688)" and "encoded by (d:P:P702)" property claims (horizontal arrows "→", "←" in the table).
• Gene pages from different species are interconnected through "ortholog (d:P:P684)" property claims (vertical arrows "↑", "↓" in the table).

The data which infobox_gene shows to readers are collected from somewhere of this interconnected Wikidata pages.

Case A

In most cases, Wikipedia article page is connected to Human gene data page. For example, Sonic hedgehog.

	Wikipedia (Article)		Wikidata (Gene)		Wikidata (Protein)
Human	Wikipedia article page Sonic hedgehog	→d:Help:Sitelinks→ ←d:Help:Sitelinks←	Human gene data page SHH (d:Q14860072)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Human protein data page Sonic hedgehog (d:Q2477760)
			↑　　　↓ ortholog (d:P:P684) ↑　　　↓
Mouse			Mouse gene data page Shh (d:Q14860079)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Mouse protein data page Sonic hedgehog (d:Q14860215)
			↑　　　↓ ortholog (d:P:P684) ↑　　　↓
⋮			⋮		⋮

Case B

In some cases, Wikipedia article page is connected to Human protein data page. For example, Reelin.

	Wikidata (Gene)		Wikidata (Protein)		Wikipedia (Article)
Human	Human gene data page RELN (d:Q414043)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Human protein data page Reelin (d:Q13561329)	→d:Help:Sitelinks→ ←d:Help:Sitelinks←	Wikipedia article page Reelin
	↑　　　↓ ortholog (d:P:P684) ↑　　　↓
Mouse	Mouse gene data page Reln (d:Q14331135)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Mouse protein data page Reelin (d:Q14331165)
	↑　　　↓ ortholog (d:P:P684) ↑　　　↓
⋮	⋮		⋮

Data location

The followings are list of data which are used in this template. Showing data example and data location in the case of Sonic hedgehog.

Data	Wikidata property	Data example	Data location				Other
			Human Gene Page	Human Protein Page	Mouse Gene Page	Mouse Protein Page
			Q14860072	Q2477760	Q14860079	Q14860215
Gene name	Label	SHH	●		●
Aliases	Aliases	HHG1, HLP3, HPE3, MCOPCB5, SMMCI, TPT, TPTPS, sonic hedgehog, Sonic hedgehog, ShhNC, sonic hedgehog signaling molecule	●		●
HGNC gene symbol	P353	SHH	●
Entrez Gene ID	P351	6469	●		●
Image	P18		●
Ensembl Gene ID	P594	ENSG00000164690	●		●
UniProt ID	P352	Q15465		●		●
EC number	P591			●		●
OMIM ID	P492	600725	●
MGI ID	P671	MGI:98297			●
HomoloGene ID	P593	30961	●		●
PDB id	P638	3HO5 3M1N 3MXW		●		●
Gene Atlas Image	P692		●
Gene ontology	P680 P681 P682	• calcium ion binding • metal ion binding • patched binding • peptidase activity • zinc ion binding • laminin-1 binding • glycosaminoglycan binding • morphogen activity • hydrolase activity • protein binding • endopeptidase activity		●		●
RefSeq RNA ID	P639	NM_000193 NM_001310462 NR_132318 NR_132319 XM_011516479 XM_011516480 XM_047420718	●		●
RefSeq Protein ID	P637	NP_000184 NP_001297391 XP_011514781 XP_011514782		●		●
Ensembl Transcript ID	P704	ENST00000472308 ENST00000297261 ENST00000430104 ENST00000435425 ENST00000441114	●		●
Chromosome	P1057	human chromosome 7	●		●
Chromosome number	P1813	7					●
Chromosome length	P2043	159345973					●
Chromosome category	P910						●
Cytogenetic location	P4196	7q36.3	●		●
Genomic start	P644	155592680	●		●
Genomic end	P645	155604967	●		●
Strand orientation	P2548	reverse strand	●		●

Similar templates

• Template:Infobox protein
• Template:Infobox enzyme
• Template:Infobox protein family
• Template:Infobox nonhuman protein
• Template:GNF Protein box - historical

See also

• d:User:ProteinBoxBot - Enormous biomedical data in Wikidata are mostly posted and maintained by this bot
• Wikipedia:Gene Wiki

External links

• BioGPS, a site that allows for automated stub creation for human gene pages using this template
• Huss, Jon W; Orozco, Camilo; Goodale, James; Wu, Chunlei; Batalov, Serge; Vickers, Tim J; Valafar, Faramarz; Su, Andrew I (8 July 2008). "A Gene Wiki for Community Annotation of Gene Function". PLoS Biology. 6 (7): e175. doi:10.1371/journal.pbio.0060175. PMID 18613750.

The above documentation is transcluded from Template:Infobox gene/doc. (edit | history)
Editors can experiment in this template's sandbox (edit | diff) and testcases (edit) pages.
Add categories to the /doc subpage. Subpages of this template.