wikipathways-collection

WikiPathways WP5087

• WikiPathways: WP5087 (classic)
• Species: Homo sapiens
• Scholia: WP5087

  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: all 5 tests OK!
• 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: 20
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 18
  • 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: 1
  • 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 8 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: 120
• Number of assertions: 241
• Number of fails: 3

Fails

Interactions with Labels

Interactions found that involve Labels: 20

• http://classic.wikipathways.org/instance/WP5087_r137400 “AP-1 dependent genes/Repair genes” with graphId e6e0b
• http://classic.wikipathways.org/instance/WP5087_r137400 “Metastasis Angiogenesis DNA methylation Genetic aberrations Cell survival & growth Replicative immortality” with graphId bcb44
• http://classic.wikipathways.org/instance/WP5087_r137400 “T-Lymphocytes” with graphId d173d
• http://classic.wikipathways.org/instance/WP5087_r137400 “Tumor-associated macrophages” with graphId abc58
• http://classic.wikipathways.org/instance/WP5087_r137400 “Integrins” with graphId fd735
• http://classic.wikipathways.org/instance/WP5087_r137400 “Cell growth” with graphId b6038
• http://classic.wikipathways.org/instance/WP5087_r137400 “Cancer-associated fibroblasts” with graphId c3977
• http://classic.wikipathways.org/instance/WP5087_r137400 “Myeloid-Derived Suppressor Cells” with graphId ef493
• http://classic.wikipathways.org/instance/WP5087_r137400 “Cell growth, differentiation” with graphId b7a91
• http://classic.wikipathways.org/instance/WP5087_r137400 “Inflammatory cytokines, cellular stresses” with graphId f66b6
• http://classic.wikipathways.org/instance/WP5087_r137400 “Tumorigenesis & Proliferation” with graphId a67ef
• http://classic.wikipathways.org/instance/WP5087_r137400 “Chemokines, Cytokines, Pro-angiogenic factors” with graphId f28b9
• http://classic.wikipathways.org/instance/WP5087_r137400 “Chemokines, Cytokines, Pro-angiogenic factors” with graphId bc02c
• http://classic.wikipathways.org/instance/WP5087_r137400 “Transcription” with graphId c8b93
• http://classic.wikipathways.org/instance/WP5087_r137400 “Degradation” with graphId b753a
• http://classic.wikipathways.org/instance/WP5087_r137400 “DNA-damage” with graphId ed5e3
• http://classic.wikipathways.org/instance/WP5087_r137400 “Stiff and fibronectin rich ECM” with graphId f5a99
• http://classic.wikipathways.org/instance/WP5087_r137400 “Other chemokines/ cytokines” with graphId f30c3
• http://classic.wikipathways.org/instance/WP5087_r137400 “Cell survival” with graphId d24dd
• http://classic.wikipathways.org/instance/WP5087_r137400 “Growth arrest” with graphId ed2d9

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

Possible MIM translocation

Interactions between identical nodes: 18

• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/idd3be9b18 “Ca2+” (https://identifiers.org/chebi/CHEBI:29108) and Ca2+” (https://identifiers.org/chebi/CHEBI:29108)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/f0b13 “FN1” (https://identifiers.org/ensembl/ENSG00000115414) and FN1” (https://identifiers.org/ensembl/ENSG00000115414)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id7d820536 “Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id7d820536 “Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id7d820536 “IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id7d820536 “IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/cf7e3 “glucose” (https://identifiers.org/chebi/CHEBI:17234) and glucose” (https://identifiers.org/chebi/CHEBI:17234)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id88ea942b “HMGB1” (https://identifiers.org/ensembl/ENSG00000189403) and HMGB1” (https://identifiers.org/ensembl/ENSG00000189403)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id63d8358f “Ca2+” (https://identifiers.org/chebi/CHEBI:29108) and Ca2+” (https://identifiers.org/chebi/CHEBI:29108)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id369f4a02 “HMGB1” (https://identifiers.org/ensembl/ENSG00000189403) and HMGB1” (https://identifiers.org/ensembl/ENSG00000189403)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id287b2937 “Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id287b2937 “Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id287b2937 “IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and Pro IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id287b2937 “IL-1B” (https://identifiers.org/ensembl/ENSG00000125538) and IL-1B” (https://identifiers.org/ensembl/ENSG00000125538)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id5141967 “CYCS” (https://identifiers.org/ensembl/ENSG00000172115) and CYCS” (https://identifiers.org/ensembl/ENSG00000172115)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/fe21b “Tryptophan” (https://identifiers.org/chebi/CHEBI:16828) and Tryptophan” (https://identifiers.org/chebi/CHEBI:16828)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/e146d “Arginine” (https://identifiers.org/chebi/CHEBI:29016) and Arginine” (https://identifiers.org/chebi/CHEBI:29016)
• http://classic.wikipathways.org/instance/WP5087_r137400 http://rdf.wikipathways.org/Pathway/WP5087_r137400/WP/Interaction/id51322b50 “MDM2” (https://identifiers.org/ensembl/ENSG00000135679) and MDM2” (https://identifiers.org/ensembl/ENSG00000135679)

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

Identifier used of a amino acid with undefined stereochemistry

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5087_r137400 Arginine CHEBI:29016

More details at https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids