wikipathways-collection

WikiPathways WP5097

• WikiPathways: WP5097 (classic)
• Species: Homo sapiens
• Scholia: WP5097

  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: 15
  • 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!
  • numericHGNCIDs: .. 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: 61
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 95
  • 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 15 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• Sec2PriProjectTests
  • outdatedHGNCSymbol: .. all OK!
  • outdatedHGNCAccessionNumber: .. all OK!
  • outdatedNCBIIdentifiers: .x we found 1 problem(s):
    • Old NCBI Gene identifiers detected: 1
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .. all OK!
  • outdatedUniProtKBIdentifiers2: .. all OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests: all 16 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 147
• Number of assertions: 293
• Number of fails: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 15

• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/f2709 (ATP6VOE2-AS1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/c0cd0 (hsa-miR-199a-5p)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/de5f3 (lnc-DENND3-2)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/e81f2 (lnc-ESRRB-1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/ba796 (lnc-FANCM-1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/d5eef (lnc-GOLGA8Q-1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/fcd36 (lnc-PMAIP1-9)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/ae947 (lnc-PYGL-1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/e7894 (lnc-RGMA-3)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/c9a30 (lnc-SCN8A-1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/f44d1 (lnc-SLC16A3-3)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/a342f (lnc-SSU72P8-2)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/f934e (lnc-U2AF2-2)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/bcac7 (lnc-ZBTB20-1)
• http://classic.wikipathways.org/instance/WP5097_r140127 http://rdf.wikipathways.org/Pathway/WP5097_r140127/DataNode/bf253 (lnc-ZFP37-1)

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/WP5097_r140127 AKT1 with datasource RefSeq

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

Interactions with Labels

Interactions found that involve Labels: 61

• http://classic.wikipathways.org/instance/WP5097_r140127 “Adhesion and F-actin polymerization” with graphId a72f0
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration of MDA-MB-231 and SKBR3 cells “ with graphId aff36
• http://classic.wikipathways.org/instance/WP5097_r140127 “Tumor-associated macrophage-induced metastasis of MDA-MB-231 cells” with graphId dc0a2
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration and invasion of MDA-MB-231 cells” with graphId e07a3
• http://classic.wikipathways.org/instance/WP5097_r140127 “Proliferation, migration, invasion and EMT in HSC6 and CAL27 cells” with graphId acdf0
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId d910d
• http://classic.wikipathways.org/instance/WP5097_r140127 “PM” with graphId db2f2
• http://classic.wikipathways.org/instance/WP5097_r140127 “Endothelial-Mesenchymal Transformation (EndMT) in HUVECs” with graphId c52fb
• http://classic.wikipathways.org/instance/WP5097_r140127 “Invasion in HEEC,ECA109, KYSE30, KYSE140 KYSE510, and TE-1 cells” with graphId a9cde
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId ad894
• http://classic.wikipathways.org/instance/WP5097_r140127 “PM” with graphId fb8d2
• http://classic.wikipathways.org/instance/WP5097_r140127 “Production of Collagen in fibroblasts” with graphId ad448
• http://classic.wikipathways.org/instance/WP5097_r140127 “In OS-RC-2 and ACHN cells” with graphId be0dd
• http://classic.wikipathways.org/instance/WP5097_r140127 “Directional migration of MDA-MB-231 cells” with graphId ff331
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration and invasion of 5637 bladder cancer cells” with graphId f8ea5
• http://classic.wikipathways.org/instance/WP5097_r140127 “Invasion and migration of A549 and H1299 cells” with graphId b68db
• http://classic.wikipathways.org/instance/WP5097_r140127 “Induction of EMT and stemness in Tu686 and FaDu cells” with graphId d4862
• http://classic.wikipathways.org/instance/WP5097_r140127 “ARF6 rich membrane protrusions” with graphId b63ac
• http://classic.wikipathways.org/instance/WP5097_r140127 “Invasion and migration of MGC-803, GES-1 and MKN28 cells” with graphId f0a72
• http://classic.wikipathways.org/instance/WP5097_r140127 “EMT in Tu686, 6-10B and FaDu cells” with graphId ff346
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration and invasion of PANC-1 and Capan-2 cells Maintenance of the Warburg effect” with graphId fc474
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration and tube formation in HUVECs” with graphId f546b
• http://classic.wikipathways.org/instance/WP5097_r140127 “Switching of CD4+CD45RO+CD25- T cells into CD4+CD25+Foxp3+ regulatory T cells” with graphId f1468
• http://classic.wikipathways.org/instance/WP5097_r140127 “PM” with graphId dae3a
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId f2fea
• http://classic.wikipathways.org/instance/WP5097_r140127 “EMT in Ishikawa cells” with graphId d7bf6
• http://classic.wikipathways.org/instance/WP5097_r140127 “Gi-alpha dependent” with graphId f3dd1
• http://classic.wikipathways.org/instance/WP5097_r140127 “F-actin polymerization in Th2 cells” with graphId a0c87
• http://classic.wikipathways.org/instance/WP5097_r140127 “Proliferation, and metastasis of HSC6 oral carcinoma cells” with graphId b8b5a
• http://classic.wikipathways.org/instance/WP5097_r140127 “PM” with graphId cc875
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId fe8ba
• http://classic.wikipathways.org/instance/WP5097_r140127 “Cytoskeleton reorganization in MDA-MB-231 cells” with graphId b8efe
• http://classic.wikipathways.org/instance/WP5097_r140127 “PM” with graphId d27c2
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId c5032
• http://classic.wikipathways.org/instance/WP5097_r140127 “ Abrogates chemotactic responses induced by their ligands” with graphId d5da1
• http://classic.wikipathways.org/instance/WP5097_r140127 “Metastasis and EMT in Tu686, 6-10B and FaDu cells” with graphId a964d
• http://classic.wikipathways.org/instance/WP5097_r140127 “Proliferation, invasion and iigration of Skov3 cells” with graphId e3fd4
• http://classic.wikipathways.org/instance/WP5097_r140127 “Hematopoiesis in myeloid long-term bone marrow cultures” with graphId fad9b
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration and invasion of BxPC-3 and PANC-1 cells” with graphId fb72c
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId b57d0
• http://classic.wikipathways.org/instance/WP5097_r140127 “NU” with graphId bafb8
• http://classic.wikipathways.org/instance/WP5097_r140127 “PM” with graphId c4d03
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId f7176
• http://classic.wikipathways.org/instance/WP5097_r140127 “EMT in HSC6 and CAL33 cells” with graphId ae0e6
• http://classic.wikipathways.org/instance/WP5097_r140127 “Lactate production in PC3 cells” with graphId fb60c
• http://classic.wikipathways.org/instance/WP5097_r140127 “Myofibroblast differentiation of breast phyllodes tumors” with graphId ef9fd
• http://classic.wikipathways.org/instance/WP5097_r140127 “Collagen production in pulmonary fibroblasts” with graphId d4114
• http://classic.wikipathways.org/instance/WP5097_r140127 “Motility of MDA-MB-231 cells” with graphId e5e31
• http://classic.wikipathways.org/instance/WP5097_r140127 “Proliferation of HSC6 and CAL27 cells” with graphId ef75c
• http://classic.wikipathways.org/instance/WP5097_r140127 “Enhances ECM adherence of MDA-MB-231 cells” with graphId aa3d8
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration of CaOV3 and OVCAR3 cells” with graphId df17f
• http://classic.wikipathways.org/instance/WP5097_r140127 “Migration & invasion of SMMC-7721 cells” with graphId b38eb
• http://classic.wikipathways.org/instance/WP5097_r140127 “NU” with graphId f53d1
• http://classic.wikipathways.org/instance/WP5097_r140127 “CY” with graphId a1a09
• http://classic.wikipathways.org/instance/WP5097_r140127 “EMT and invasion of MDA-MB-231 and MCF-7 cells” with graphId e5688
• http://classic.wikipathways.org/instance/WP5097_r140127 “EMT in MDA-MB-231 and MCF-7 cells” with graphId c0b24
• http://classic.wikipathways.org/instance/WP5097_r140127 “Polymerization of F-actin and Cytoskeleton reorganization in A549 and H1299 cells” with graphId af3f5
• http://classic.wikipathways.org/instance/WP5097_r140127 “Proliferation and differentiation in Tu686, 6-10B and FaDu cells” with graphId c3e31
• http://classic.wikipathways.org/instance/WP5097_r140127 “Induces stem cell-like characteristics in HSC6, CAL33 and SCC15 cells” with graphId d6a0b
• http://classic.wikipathways.org/instance/WP5097_r140127 “Proliferation and migration of MG63 and 143B osteosarcoma cells” with graphId d8633
• http://classic.wikipathways.org/instance/WP5097_r140127 “Adhesion, migration and invasion of MCF-7 cells” with graphId c9441

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

Interactions with unconnected points

Interactions with unconnected points: 95

• http://classic.wikipathways.org/instance/WP5097_r140127

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

NCBI Gene identifier has been retracted

Old NCBI Gene identifiers detected: 1

• http://classic.wikipathways.org/instance/WP5097_r140127 LINC00266-3 has NCBI Gene 441123 but has been replaced by 107105278

More details at https://www.wikipathways.org/WikiPathwaysCurator/Sec2PriProjectTests/outdatedNCBIIdentifiers