wikipathways-collection

WikiPathways WP4298

• WikiPathways: WP4298 (classic)
• Species: Homo sapiens
• Scholia: WP4298

  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: 23
  • 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: 50
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • 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: 23

• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/cccec (135 S A-particle)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/b3f8b (2A^PRO)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/eb98b (3C^PRO)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/dd6f4 (IgG)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/ea901 (IgG)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/bde2d (MEK 1/2)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/d9564 (MHCII )
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/eac49 (MK2)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/bd4fb (MKK 3/6)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/a915e (MKK 4/7)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/f3e5d (Macrophage )
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/ac79f (Matrix metalloproteinases)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/f6365 (NF-kB)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/af643 (NLRP3)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/d947f (PAR)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/e8d23 (Pro-IL-18)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/a765f (T cell receptor alpha chain V region)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/be2de (T-cell receptor beta chain V region)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/da5cd (Tyrosine kinase)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/a4ca8 (Viral entry CVB3)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/dde75 (hsp27)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/e6b96 (peptidoglycan muramyl dipeptide)
• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/DataNode/d23c9 (pro-IL-1beta)

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/WP4298_r134291 IL1 with datasource Pfam

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

Interactions with Labels

Interactions found that involve Labels: 50

• http://classic.wikipathways.org/instance/WP4298_r134291 “Antigen presenting cell” with graphId f64c2
• http://classic.wikipathways.org/instance/WP4298_r134291 “Viral antigens” with graphId c772d
• http://classic.wikipathways.org/instance/WP4298_r134291 “AD2” with graphId b831b
• http://classic.wikipathways.org/instance/WP4298_r134291 “Decreased force transmission Increased cell permeability” with graphId a000e
• http://classic.wikipathways.org/instance/WP4298_r134291 “Myocyte dysfunction” with graphId e7ae3
• http://classic.wikipathways.org/instance/WP4298_r134291 “Increased expr. ? Promotes tissue fibrosis ? “ with graphId e8594
• http://classic.wikipathways.org/instance/WP4298_r134291 “Loss of mechanical stability of the cell” with graphId d9500
• http://classic.wikipathways.org/instance/WP4298_r134291 “Mitochondrion” with graphId a9a73
• http://classic.wikipathways.org/instance/WP4298_r134291 “Viral replication, inactivation of p21ras” with graphId ad0e2
• http://classic.wikipathways.org/instance/WP4298_r134291 “CVB1” with graphId cd959
• http://classic.wikipathways.org/instance/WP4298_r134291 “Autoreactive antibodies” with graphId af1dc
• http://classic.wikipathways.org/instance/WP4298_r134291 “HIV-1 “ with graphId ea662
• http://classic.wikipathways.org/instance/WP4298_r134291 “HIV” with graphId af64a
• http://classic.wikipathways.org/instance/WP4298_r134291 “Virus-specific antibodies” with graphId d8910
• http://classic.wikipathways.org/instance/WP4298_r134291 “HIV-2 “ with graphId ed8a7
• http://classic.wikipathways.org/instance/WP4298_r134291 “Actin reorganization” with graphId c24c8
• http://classic.wikipathways.org/instance/WP4298_r134291 “Host protein synthesis shutoff induction of CPE” with graphId f09b0
• http://classic.wikipathways.org/instance/WP4298_r134291 “antigen” with graphId c7b21
• http://classic.wikipathways.org/instance/WP4298_r134291 “Symptomatic arrhythmias” with graphId d64a6
• http://classic.wikipathways.org/instance/WP4298_r134291 “Overproduction of fibrofatty tissue in myocardium” with graphId a9e28
• http://classic.wikipathways.org/instance/WP4298_r134291 “Immune-mediated myocyte damage” with graphId bab8d
• http://classic.wikipathways.org/instance/WP4298_r134291 “Mature secreted forms” with graphId dfd16
• http://classic.wikipathways.org/instance/WP4298_r134291 “Decreased expr.” with graphId abbf8
• http://classic.wikipathways.org/instance/WP4298_r134291 “Myocyte necrosis Fibrosis Myocyte atrophy” with graphId cad70
• http://classic.wikipathways.org/instance/WP4298_r134291 “Suppresses cytopathic effects” with graphId cdc0a
• http://classic.wikipathways.org/instance/WP4298_r134291 “Sarcomer” with graphId cc327
• http://classic.wikipathways.org/instance/WP4298_r134291 “Inflammation” with graphId f72d5
• http://classic.wikipathways.org/instance/WP4298_r134291 “Coxsackie B virus” with graphId ed816
• http://classic.wikipathways.org/instance/WP4298_r134291 “CVB3” with graphId e5596
• http://classic.wikipathways.org/instance/WP4298_r134291 “Chaotic apoptosis and/or necrosis” with graphId d1968
• http://classic.wikipathways.org/instance/WP4298_r134291 “antigen” with graphId a6c51
• http://classic.wikipathways.org/instance/WP4298_r134291 “Degradation” with graphId e2591
• http://classic.wikipathways.org/instance/WP4298_r134291 “Cell cycle arrest” with graphId d6817
• http://classic.wikipathways.org/instance/WP4298_r134291 “Adenovirus “ with graphId e1a6f
• http://classic.wikipathways.org/instance/WP4298_r134291 “Matrix degradation” with graphId c2c4e
• http://classic.wikipathways.org/instance/WP4298_r134291 “Primary profibrotic cytokine” with graphId d1f14
• http://classic.wikipathways.org/instance/WP4298_r134291 “DNA fragmentation within nucleus” with graphId fbb95
• http://classic.wikipathways.org/instance/WP4298_r134291 “Dystrophin deficiency leads to loss of the sarcoglycan complex pre-cursor to DCM” with graphId a213f
• http://classic.wikipathways.org/instance/WP4298_r134291 “Viral progeny release” with graphId ad04a
• http://classic.wikipathways.org/instance/WP4298_r134291 “Enterovirus-induced cardiomyopathy” with graphId b5d55
• http://classic.wikipathways.org/instance/WP4298_r134291 “Phosphorylated dimers move to nucleus stimulate gene expression” with graphId d65f2
• http://classic.wikipathways.org/instance/WP4298_r134291 “Max. release of progeny virion” with graphId dce91
• http://classic.wikipathways.org/instance/WP4298_r134291 “Viral genomic RNA” with graphId f36cd
• http://classic.wikipathways.org/instance/WP4298_r134291 “t-Bid” with graphId b7858
• http://classic.wikipathways.org/instance/WP4298_r134291 “Viral replication” with graphId f0317
• http://classic.wikipathways.org/instance/WP4298_r134291 “Cardiac antigens” with graphId cfcfa
• http://classic.wikipathways.org/instance/WP4298_r134291 “Increased expr.” with graphId a7adf
• http://classic.wikipathways.org/instance/WP4298_r134291 “Cellular activation” with graphId ad96f
• http://classic.wikipathways.org/instance/WP4298_r134291 “beta catenin pathway” with graphId da3aa
• http://classic.wikipathways.org/instance/WP4298_r134291 “Degeneration” with graphId c2dac

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP4298_r134291 http://rdf.wikipathways.org/Pathway/WP4298_r134291/WP/Interaction/ida31723f6 “Ca2+” (https://identifiers.org/hmdb/HMDB0000464) and Ca2+” (https://identifiers.org/hmdb/HMDB0000464)

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