SARS-CoV-2-Queries

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El humano

Genes y proteínas que interactúan

Comprender los procesos biológicos por los cuales funciona el virión CoV requiere conocer qué genes y proteínas humanos están involucrados. Esto es hacia la siguiente sección, por supuesto, es posible que primero deseemos saber qué dice la literatura aquí (la anotación aún es limitada):

SPARQL sparql/humanInteractionCounts.rq (ejecutar, editar)

SELECT ?virus ?virusLabel ?gene ?geneLabel ?count WITH {
  SELECT ?virus ?gene (COUNT(DISTINCT ?work) AS ?count) WHERE {
    ?virus wdt:P171+ wd:Q57751738 .
    ?work wdt:P921 ?virus, ?gene .
    ?gene wdt:P703 wd:Q15978631 .
    { ?gene wdt:P31 wd:Q7187 } UNION { ?gene wdt:P31 wd:Q8054 }
  } GROUP BY ?virus ?gene
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "es,en". }
}
ORDER BY DESC(?count) ?virus ?gene

Esto nos da estos números de documentos:

virus gene count
SARS-CoV-2 (edit) Angiotensin I converting enzyme 2 (edit) 19
SARS-CoV-2 (edit) Transmembrane serine protease 2 (edit) 7
SARS-CoV (edit) Angiotensin I converting enzyme 2 (edit) 5
SARS-CoV (edit) Transmembrane serine protease 2 (edit) 3
Betacoronavirus (edit) Angiotensin I converting enzyme 2 (edit) 2
SARS coronavirus (edit) Angiotensin I converting enzyme 2 (edit) 2
MERS-CoV (edit) DPP-4 (edit) 2
SARS-CoV-2 (edit) Enzima convertidora de angiotensina II (edit) 2
SARS-CoV-2 (edit) TMPRSS2 (edit) 2
SARS-CoV-2 (edit) Furin, paired basic amino acid cleaving enzyme (edit) 2
Human coronavirus 229E (edit) TMPRSS2 (edit) 1
Human coronavirus 229E (edit) Transmembrane serine protease 2 (edit) 1
Human coronavirus 229E (edit) Peptidylprolyl isomerase A (edit) 1
Human coronavirus 229E (edit) CD13 (edit) 1
Human coronavirus 229E (edit) Angiotensin I converting enzyme 2 (edit) 1
SARS coronavirus (edit) MASP2 (edit) 1
SARS coronavirus (edit) factor de necrosis tumoral (edit) 1
SARS coronavirus (edit) Interferon induced transmembrane protein 3 (edit) 1
SARS coronavirus (edit) Interferon induced transmembrane protein 2 (edit) 1
SARS coronavirus (edit) Interferon induced transmembrane protein 1 (edit) 1
MERS-CoV (edit) Transmembrane serine protease 2 (edit) 1
SARS-CoV-2 (edit) IL6 (edit) 1
SARS-CoV-2 (edit) FURIN (edit) 1
SARS-CoV-2 (edit) MX1 (edit) 1
SARS-CoV-2 (edit) PIKFYVE (edit) 1
SARS-CoV-2 (edit) Transmembrane serine protease 4 (edit) 1
SARS-CoV-2 (edit) Translocase of outer mitochondrial membrane 70 (edit) 1
SARS-CoV-2 (edit) Factor de von Willebrand (edit) 1
SARS-CoV-2 (edit) ADAMTS13 (edit) 1
SARS-CoV-2 (edit) Heme oxygenase 1 (edit) 1
Coronavirus Humana NL63 (edit) Angiotensin I converting enzyme 2 (edit) 1
SARS-CoV (edit) MASP2 (edit) 1
SARS-CoV (edit) factor de necrosis tumoral (edit) 1
SARS-CoV (edit) C-type lectin domain family 4 member G (edit) 1
SARS-CoV (edit) C-type lectin domain family 4 member M (edit) 1
SARS-CoV (edit) Interferon induced transmembrane protein 3 (edit) 1
SARS-CoV (edit) Interferon induced transmembrane protein 2 (edit) 1
SARS-CoV (edit) Interferon induced transmembrane protein 1 (edit) 1
SARS-CoV (edit) BCL2 like 1 (edit) 1
SARS-CoV (edit) BCL2 associated X, apoptosis regulator (edit) 1

Si desea ver los documentos específicos (una lista creciente), use esta consulta:

SPARQL sparql/humanInteractions.rq (ejecutar, editar)

SELECT ?date ?virus ?virusLabel ?gene ?geneLabel ?work ?workLabel ?doi WITH {
  SELECT (MAX(?dates) as ?date) ?virus ?gene ?work WHERE {
    ?virus wdt:P171+ wd:Q57751738 .
    ?work wdt:P921 ?virus, ?gene .  
    OPTIONAL { ?work wdt:P577 ?dates . }
    ?gene wdt:P703 wd:Q15978631 .   
    { ?gene wdt:P31 wd:Q7187 } UNION { ?gene wdt:P31 wd:Q8054 }
  } GROUP BY ?virus ?gene ?work
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  OPTIONAL { ?work wdt:P356 ?doi . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "es,en". }
}
ORDER BY DESC(?date) ?doi ?virus ?gene

Procesos biológicos

WikiPathways [1] es uno de los proyectos involucrados en el esfuerzo de curación internacional de #covidpathways COVID-19 y las contribuciones de WikiPathways se pueden encontrar en este portal.

Vías moleculares de Reactome [2] y WikiPathways están indexadas en Wikidata, y podemos consultar las vías que tienen genes y proteínas de coronavirus humanos:

SPARQL sparql/pathways.rq (ejecutar, editar)

SELECT ?virus ?virusLabel ?thing ?thingLabel ?pathway ?pathwayLabel WHERE {
  VALUES ?virus {
    wd:Q82069695 # SARS-CoV-2
    wd:Q16983360 # HKU1
    wd:Q16991954 # OC43
    wd:Q8351095  # NL63 
    wd:Q16983356 # 229E
    wd:Q4902157  # MERS-CoV
    wd:Q278567   # SARS-CoV
  }
  ?thing wdt:P703 ?virus .
  ?pathway wdt:P31 wd:Q4915012 ; wdt:P527 ?thing .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "es,en". }
} ORDER BY ASC(?virus) ASC(?thing) ASC(?pathway)

Actualmente, esto enumera las siguientes vías, pero con la curación activa, se espera que también crezca rápidamente:

virus thing pathway
SARS coronavirus (edit) Protein 3a [SARS-Cov] (edit) Host-pathogen interaction of human corona viruses - apoptosis (edit)
SARS coronavirus (edit) Protein 3a [SARS-Cov] (edit) Host-pathogen interaction of human corona viruses - MAPK signaling (edit)
SARS coronavirus (edit) Protein 3a [SARS-Cov] (edit) Host-pathogen interaction of human corona viruses - Interferon induction (edit)
SARS-CoV-2 (edit) ORF9c protein [SARS CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) S1 Subunit of Spike Protein (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) S1 Subunit of Spike Protein (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) S1 Subunit of Spike Protein (edit) SARS-CoV-2 altering angiogenesis via NRP1 (edit)
SARS-CoV-2 (edit) S2 Subunit of Spike Protein (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) S2 Subunit of Spike Protein (edit) SARS-CoV-2 altering angiogenesis via NRP1 (edit)
SARS-CoV-2 (edit) S2 Subunit of Spike Protein (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) A draft map of SARS-COV-2 signaling pathway map (edit)
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) Pathogenesis of SARS-CoV-2 Mediated by nsp9-nsp10 Complex (edit)
SARS-CoV-2 (edit) non-structural protein 15 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) non-structural protein 15 [SARS-CoV-2] (edit) Endoplasmic reticulum stress response in Coronavirus infection (edit)
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) Type I Interferon Induction and Signaling During SARS-CoV-2 Infection (edit)
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) Host-pathogen interaction of human corona viruses - Interferon induction (edit)
SARS-CoV-2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) SARS-CoV-2 altering angiogenesis via NRP1 (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) Downregulation of ACE2 expression by SARS-CoV infection and SARS-CoV Spike protein (edit)
SARS-CoV-2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Viroporin 3a [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) Viroporin 3a [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF1a polyprotein (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Protein 7a [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF8 protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF6 protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF10 protein [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) ORF10 protein [SARS-CoV-2] (edit) Hijack of Ubiquitination by SARS-CoV-2 (edit)
SARS-CoV-2 (edit) Protein ORF9b [SARS-CoV-2] (edit) SARS-CoV-2 mitochondrial interactions (edit)
SARS-CoV-2 (edit) Protein ORF9b [SARS-CoV-2] (edit) SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response (edit)
SARS-CoV-2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) Pathogenesis of SARS-CoV-2 Mediated by nsp9-nsp10 Complex (edit)
SARS-CoV-2 (edit) SARS-CoV-2 NSP9 complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike - human ACE2 receptor complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike - human ACE2-SLC6A19 complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike protein complex (edit) Linoleic acid metabolism known to be affected by coronavirus infection (edit)
SARS-CoV-2 (edit) SARS-CoV-2 Spike protein complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 main protease complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 NSP10-NSP16 2'-O-methyltransferase complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) SARS-CoV-2 NSP3-NSP4-NSP6 complex (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) nsp1 from SARS-CoV-2 inhibits translation initiation in the host cell (edit)
SARS-CoV-2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) SARS-CoV-2 and COVID-19 Pathway (edit)
SARS-CoV-2 (edit) Uncharacterized protein 14 (edit) SARS-CoV-2 and COVID-19 Pathway (edit)

Referencias

  1. Slenter DN, Kutmon M, Hanspers K, Hanspers K, Riutta A, Windsor J, et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. NAR. 2018 Jan 4;46(D1):D661–7. doi:10.1093/NAR/GKX1064 (Scholia)
  2. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, et al. The Reactome pathway knowledgebase. NAR. 2014 Jan;42(Database issue):D472-7. doi:10.1093/NAR/GKT1102 (Scholia)