Question: How to identify ZNFs from a gene list?
0
gravatar for Arindam Ghosh
10 weeks ago by
Arindam Ghosh250
India
Arindam Ghosh250 wrote:

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.

pfam uniprot protein domain • 148 views
ADD COMMENTlink modified 10 weeks ago by Pierre Lindenbaum128k • written 10 weeks ago by Arindam Ghosh250
1
gravatar for genomax
10 weeks ago by
genomax84k
United States
genomax84k wrote:

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.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by genomax84k
0
gravatar for Pierre Lindenbaum
10 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

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
(...)
ADD COMMENTlink written 10 weeks ago by Pierre Lindenbaum128k
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