wikipathways-collection

WikiPathways WP4657

• WikiPathways: WP4657 (classic)
• Species: Homo sapiens
• Scholia: WP4657

  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: 1
• 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: 12
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 2
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • achiralAminoAcids: .x we found 1 problem(s):
    • Metabolites with ChEBI identifiers of achiral amino acids: 4
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • metaboliteAlsoOtherType: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all 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: 119
• Number of assertions: 239
• Number of fails: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP4657_r128796 http://rdf.wikipathways.org/Pathway/WP4657_r128796/DataNode/f74de (BCR(KLHL22) E3 ubiquitin ligase complex)

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: 1

http://classic.wikipathways.org/instance/WP4657_r128796 Syntaxin with datasource Pfam

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

Interactions with Labels

Interactions found that involve Labels: 12

• http://classic.wikipathways.org/instance/WP4657_r128796 “Candidate gene for oculo-auriculo-vertebral spectrum (OAVS) asymmetry” with graphId d210a
• http://classic.wikipathways.org/instance/WP4657_r128796 “Increased expression in gastric and other cancers” with graphId a8b23
• http://classic.wikipathways.org/instance/WP4657_r128796 “cell division cycle regulatory protein cytoskeleton organization neurotransmitter release” with graphId b65a3
• http://classic.wikipathways.org/instance/WP4657_r128796 “Circadian expression cycle” with graphId fc30e
• http://classic.wikipathways.org/instance/WP4657_r128796 “unknown function ubiquitin carboxyl-terminal hydrolase activity” with graphId e3c63
• http://classic.wikipathways.org/instance/WP4657_r128796 “Neuronal inhibition” with graphId abfbd
• http://classic.wikipathways.org/instance/WP4657_r128796 “unclear function possibly involved in mitochondria function neurodevelopment” with graphId f35c2
• http://classic.wikipathways.org/instance/WP4657_r128796 “Axonal growth” with graphId df21d
• http://classic.wikipathways.org/instance/WP4657_r128796 “unknown function” with graphId c12c8
• http://classic.wikipathways.org/instance/WP4657_r128796 “exact function unknown” with graphId beca6
• http://classic.wikipathways.org/instance/WP4657_r128796 “Exocytosis” with graphId dff0a
• http://classic.wikipathways.org/instance/WP4657_r128796 “unknown function possible candidate for retinitis pigmentosa” with graphId f89f6

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP4657_r128796 http://rdf.wikipathways.org/Pathway/WP4657_r128796/WP/Interaction/b954e “FOXC1” (https://identifiers.org/ensembl/ENSG00000054598) and FOXC1” (https://identifiers.org/ensembl/ENSG00000054598)
• http://classic.wikipathways.org/instance/WP4657_r128796 http://rdf.wikipathways.org/Pathway/WP4657_r128796/WP/Interaction/b4cf6 “Citrate” (https://identifiers.org/chebi/CHEBI:133748) and Citrate” (https://identifiers.org/chebi/CHEBI:133748)

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

MetabolitesTests.achiralAminoAcids

Metabolites with ChEBI identifiers of achiral amino acids: 4

http://classic.wikipathways.org/instance/WP4657_r128796 Arginine CHEBI:29016
http://classic.wikipathways.org/instance/WP4657_r128796 Glutamine CHEBI:28300
http://classic.wikipathways.org/instance/WP4657_r128796 Lysine CHEBI:25094
http://classic.wikipathways.org/instance/WP4657_r128796 Proline CHEBI:26271