wikipathways-collection

WikiPathways WP4341

• WikiPathways: WP4341 (classic)
• Species: Homo sapiens
• Scholia: WP4341

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 1
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all 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: 17
• 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: 5
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 11
  • 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: all 6 tests 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: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/DataNode/ce3fe (VSE)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

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: 17

http://classic.wikipathways.org/instance/WP4341_r134957 PIK3CD with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PLA2 with datasource InterPro
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3R1 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 AKT2 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3C3 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3CG with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3C2G with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3C2B with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 AKT3 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3C2A with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3CA with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3R5 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 AKT1 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3R4 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3R2 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3R3 with datasource GenBank
http://classic.wikipathways.org/instance/WP4341_r134957 PIK3CB with datasource GenBank

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

Interactions with Labels

Interactions found that involve Labels: 5

• http://classic.wikipathways.org/instance/WP4341_r134957 “Stress” with graphId a70e0
• http://classic.wikipathways.org/instance/WP4341_r134957 “TLR2/4/8 ligands” with graphId b4453
• http://classic.wikipathways.org/instance/WP4341_r134957 “Cell death” with graphId eebf1
• http://classic.wikipathways.org/instance/WP4341_r134957 “?” with graphId b53b9
• http://classic.wikipathways.org/instance/WP4341_r134957 “VDR transcription” with graphId da643

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

Possible MIM translocation

Interactions between identical nodes: 11

• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRn” (https://identifiers.org/ensembl/ENSG00000111424) and VDRn” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRn” (https://identifiers.org/ensembl/ENSG00000111424) and VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRn” (https://identifiers.org/ensembl/ENSG00000111424) and VDR” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424) and VDRn” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424) and VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424) and VDR” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDR” (https://identifiers.org/ensembl/ENSG00000111424) and VDRn” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDR” (https://identifiers.org/ensembl/ENSG00000111424) and VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDR” (https://identifiers.org/ensembl/ENSG00000111424) and VDR” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/ide241ec12 “25D” (https://identifiers.org/hmdb/HMDB0003550) and 25D” (https://identifiers.org/hmdb/HMDB0003550)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id8155bdbf “CYP27B1” (https://identifiers.org/ensembl/ENSG00000111012) and CYP27B1” (https://identifiers.org/ensembl/ENSG00000111012)

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