How to identify ZNFs from a gene list?
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16 months ago
Arindam Ghosh ▴ 370

Is there a way to identify which of the genes in a list encode for zinc finger proteins (human)? Do the names of all ZNFs start with ZNF? I guess this is a no.

protein domain pfam uniprot • 382 views
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16 months ago
GenoMax 104k

A search at UniProt brings up these proteins for human. You can decide if you want to use reviewed (SwissProt) or computationally predicted (TrEMBL) proteins.

You could also search BioMart (human genome) using these Interpro Accession numbers for Zinc Finger to get gene names.

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16 months ago

using uniprot+SPARQL: https://sparql.uniprot.org/

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
PREFIX uberon: <http://purl.obolibrary.org/obo/uo#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX sp: <http://spinrdf.org/sp#>
PREFIX slm: <https://swisslipids.org/rdf/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX sh: <http://www.w3.org/ns/shacl#>
PREFIX schema: <http://schema.org/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
PREFIX patent: <http://data.epo.org/linked-data/def/patent/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX orthodbGroup: <http://purl.orthodb.org/odbgroup/>
PREFIX orthodb: <http://purl.orthodb.org/>
PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX mnet: <https://rdf.metanetx.org/mnet/>
PREFIX mesh: <http://id.nlm.nih.gov/mesh/>
PREFIX keywords: <http://purl.uniprot.org/keywords/>
PREFIX identifiers: <http://identifiers.org/>
PREFIX glyconnect: <https://purl.org/glyconnect/>
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX eunisSpecies: <http://eunis.eea.europa.eu/rdf/species-schema.rdf#>
PREFIX ensembltranscript: <http://rdf.ebi.ac.uk/resource/ensembl.transcript/>
PREFIX ensemblterms: <http://rdf.ebi.ac.uk/terms/ensembl/>
PREFIX ensemblprotein: <http://rdf.ebi.ac.uk/resource/ensembl.protein/>
PREFIX ensemblexon: <http://rdf.ebi.ac.uk/resource/ensembl.exon/>
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/>
PREFIX ec: <http://purl.uniprot.org/enzyme/>
PREFIX dc: <http://purl.org/dc/terms/>
PREFIX codoa: <http://purl.glycoinfo.org/ontology/codao#>
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX chebihash: <http://purl.obolibrary.org/obo/chebi#>
PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX allie: <http://allie.dbcls.jp/>
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT DISTINCT ?protein ?title 
WHERE 
{
    ?protein a up:Protein .
    ?protein up:organism <http://purl.uniprot.org/taxonomy/9606> .
    ?protein up:mnemonic ?title .
    ?protein up:annotation ?annotation .
    ?annotation  a up:Zinc_Finger_Annotation .

}

.

http://purl.uniprot.org/uniprot/Q15057  "ACAP2_HUMAN"xsd:string
http://purl.uniprot.org/uniprot/O95376  "ARI2_HUMAN"xsd:string
http://purl.uniprot.org/uniprot/Q6ZSZ5  "ARHGI_HUMAN"xsd:string
http://purl.uniprot.org/uniprot/Q8N1W1  "ARG28_HUMAN"xsd:string
http://purl.uniprot.org/uniprot/Q8TF27  "AGA11_HUMAN"xsd:string
(...)
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