wikipathways-collection

WikiPathways WP2292

• WikiPathways: WP2292 (classic)
• Species: Mus musculus

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: …. all OK!
  • nonNumericHGNCAccessionNumbers: .. all OK!
  • genesWithoutEnsemblMapping: .x we found 1 problem(s):
    • The following genes with an identifier have been found but that do not have a mapping to Ensembl: 9
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 4
  • possibleTranslocations: .. all OK!
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 7 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests
  • nonNumericPubMedIDs: .. all OK!
  • unexpectedPubMedIdentifier: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all OK!
  • outdatedPubMedIdentifiers: .. all OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 20
• Number of tests: 118
• Number of assertions: 237
• Number of fails: 3

Fails

Genes with identifier but no Ensembl identifier mapping

The following genes with an identifier have been found but that do not have a mapping to Ensembl: 9

http://classic.wikipathways.org/instance/WP2292_r97515 Gm12844 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Gm15776 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Ccl21c with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Gm4356 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 c-C motif chemokine 12-like with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Gm2023 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Cxcl11 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Gm3785 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2292_r97515 Gm5741 with datasource Entrez Gene

More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping

Interactions with Labels

Interactions found that involve Labels: 4

• http://classic.wikipathways.org/instance/WP2292_r97515 “Degradation Chemotaxis NO induction” with graphId ff4a4
• http://classic.wikipathways.org/instance/WP2292_r97515 “Cytokine production Cellular growth and differentiation Cell survival Migration Apoptosis” with graphId b94aa
• http://classic.wikipathways.org/instance/WP2292_r97515 “Receptor internalization” with graphId a51d1
• http://classic.wikipathways.org/instance/WP2292_r97515 “ROS production” with graphId d8902

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP2292_r97515 ‘Chemokine signaling pathway’ in Mus musculus has zero references;

More details at https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference