wikipathways-collection
WikiPathways WP5434
- WikiPathways: WP5434 (classic)
- Species: Homo sapiens
- Scholia: WP5434
Tests
- CASMetabolitesTests: all 2 tests OK!
- ChEBIMetabolitesTests: all 5 tests OK!
- ChemSpiderTests: all 2 tests OK!
- DataNodesTests
- dataNodesWithoutIdentifier: .x we found 1 problem(s):
- 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):
- 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):
- possibleTranslocations: .x we found 1 problem(s):
- 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
- nonNumericPubMedIDs: .. all OK!
- unexpectedPubMedIdentifier: .. all OK!
- zeroPubMedIDs: .. all OK!
- atLeastOneReference: .x we found 1 problem(s):
- citesRetractedArticle: .. all OK!
- outdatedPubMedIdentifiers: .. all 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: 5
Fails
Data nodes without an identifier
The following DataNodes have no identifier: 6
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/DataNode/e6a25 (Adherens junction)
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/DataNode/d4c24 (Calcium signaling pathway)
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/DataNode/feed7 (HIF-1 signaling pathway)
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/DataNode/f745a (Jak-STAT signaling pathway)
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/DataNode/edeec (cAMP signaling pathway)
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/DataNode/c7405 (p53 signaling pathway)
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: 3
http://classic.wikipathways.org/instance/WP5434_r135326 CALML2 with datasource HGNC
http://classic.wikipathways.org/instance/WP5434_r135326 GSTT1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5434_r135326 CALML1 with datasource HGNC
More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping
Interactions with Labels
Interactions found that involve Labels: 16
- http://classic.wikipathways.org/instance/WP5434_r135326 “Sustained angiogenesis” with graphId e0fb5
- http://classic.wikipathways.org/instance/WP5434_r135326 “Ligands” with graphId d7ce6
- http://classic.wikipathways.org/instance/WP5434_r135326 “Telomeric DNA repeats” with graphId a5033
- http://classic.wikipathways.org/instance/WP5434_r135326 “Evaiding apoptosis” with graphId bccad
- http://classic.wikipathways.org/instance/WP5434_r135326 “RARa target genes” with graphId a3712
- http://classic.wikipathways.org/instance/WP5434_r135326 “Block of differentiation” with graphId cd32c
- http://classic.wikipathways.org/instance/WP5434_r135326 “Proliferation” with graphId e085a
- http://classic.wikipathways.org/instance/WP5434_r135326 “DNA damage” with graphId f7cde
- http://classic.wikipathways.org/instance/WP5434_r135326 “Genomic damage” with graphId f5bfe
- http://classic.wikipathways.org/instance/WP5434_r135326 “Carcinogens” with graphId a91b5
- http://classic.wikipathways.org/instance/WP5434_r135326 “Genomic instability” with graphId c4abf
- http://classic.wikipathways.org/instance/WP5434_r135326 “Resistance to chemotherapy” with graphId af183
- http://classic.wikipathways.org/instance/WP5434_r135326 “Immortality” with graphId f421c
- http://classic.wikipathways.org/instance/WP5434_r135326 “Tissue invasion and metastasis” with graphId de632
- http://classic.wikipathways.org/instance/WP5434_r135326 “Insesitivity to anti-growth signals” with graphId f8ce5
- http://classic.wikipathways.org/instance/WP5434_r135326 “?” with graphId fde17
More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels
Possible MIM translocation
Interactions between identical nodes: 1
- http://classic.wikipathways.org/instance/WP5434_r135326 http://rdf.wikipathways.org/Pathway/WP5434_r135326/WP/Interaction/id602ce955 “Estradiol” (https://identifiers.org/hmdb/HMDB0000151) and Estradiol” (https://identifiers.org/hmdb/HMDB0000151)
More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations
At least one reference
Found 1 pathways with zero (PubMed) references
- http://classic.wikipathways.org/instance/WP5434_r135326 ‘Cancer pathways’ in Homo sapiens has zero references;
More details at https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference