def test_no_infer_protein_fusion(self): """Test that no gene is inferred from a RNA fusion node.""" partner5p = Protein(n(), n()) partner3p = Protein(n(), n()) p = protein_fusion(partner_3p=partner3p, partner_5p=partner5p) graph = BELGraph() graph.add_node_from_data(p) self.assertEqual(1, graph.number_of_nodes()) self.assertEqual(0, graph.number_of_edges()) enrich_protein_and_rna_origins(graph) self.assertEqual(1, graph.number_of_nodes()) self.assertEqual(0, graph.number_of_edges())
def test_names_fusions(self): """Test that names inside fusions are still found by the iterator.""" graph = BELGraph() graph.namespace_url['HGNC'] = 'http://dummy' node = protein_fusion(partner_5p=protein(name='A', namespace='HGNC'), range_5p=fusion_range('p', 1, 15), partner_3p=protein(name='B', namespace='HGNC'), range_3p=fusion_range('p', 1, 100)) graph.add_node_from_data(node) result = { 'A': 1, 'B': 1, } self.assertEqual(set(result), get_names_by_namespace(graph, 'HGNC')) self.assertEqual(result, count_names_by_namespace(graph, 'HGNC'))
kng1 = protein('HGNC', 'KNG1') kallidin = abundance('CHEBI', 'Kallidin') pla2_family = protein('SFAM', 'PLA2 Family') kng1_to_kallidin = reaction(reactants=[kng1], products=[kallidin]) example_graph.add_increases(inflammatory_process, kng1_to_kallidin, citation=c4, evidence=e4) example_graph.add_increases(kallidin, bdkrb1, citation=c4, evidence=e4, object_modifier=catalytic_activity) example_graph.add_increases(bdkrb1, pla2_family, citation=c4, evidence=e4, subject_modifier=catalytic_activity, object_modifier=catalytic_activity) c5 = '10866298' e5 = 'We found that PD180970 inhibited in vivo tyrosine phosphorylation of p210Bcr-Abl (IC50 = 170 nM) and the p210BcrAbl substrates Gab2 and CrkL (IC50 = 80 nM) in human K562 chronic myelogenous leukemic cells. In vitro, PD180970 potently inhibited autophosphorylation of p210Bcr-Abl (IC50 = 5 nM) and the kinase activity of purified recombinant Abl tyrosine kinase (IC50 = 2.2 nM).' """ SET Species = 9606 SET Citation = {"PubMed","Cancer Res 2000 Jun 15 60(12) 3127-31","10866298","","",""} kin(p(HGNC:BCR,fus(HGNC:ABL1))) directlyIncreases p(HGNC:CRKL,pmod(P,Y)) kin(p(HGNC:BCR,fus(HGNC:ABL1))) directlyIncreases p(HGNC:GAB2,pmod(P,Y)) """ bcr_abl1_fus = protein_fusion(partner_5p=protein('HGNC', 'BCR'), partner_3p=protein('HGNC', 'ABL1')) crkl_ph = protein('HGNC', 'CRKL', variants=[pmod('Ph', 'Tyr')]) gab2_ph = protein('HGNC', 'GAB2', variants=[pmod('Ph', 'Tyr')]) example_graph.add_directly_increases(bcr_abl1_fus, crkl_ph, citation=c5, evidence=e5, annotations={'Species': '9606', 'Confidence': 'High'}, subject_modifier=kinase_activity) example_graph.add_directly_increases(bcr_abl1_fus, gab2_ph, citation=c5, evidence=e5, annotations={'Species': '9606'}, subject_modifier=kinase_activity)
evidence=e4, subject_modifier=catalytic_activity, object_modifier=catalytic_activity) c5 = '10866298' e5 = 'We found that PD180970 inhibited in vivo tyrosine phosphorylation of p210Bcr-Abl (IC50 = 170 nM) and the p210BcrAbl substrates Gab2 and CrkL (IC50 = 80 nM) in human K562 chronic myelogenous leukemic cells. In vitro, PD180970 potently inhibited autophosphorylation of p210Bcr-Abl (IC50 = 5 nM) and the kinase activity of purified recombinant Abl tyrosine kinase (IC50 = 2.2 nM).' """ SET Species = 9606 SET Citation = {"PubMed","Cancer Res 2000 Jun 15 60(12) 3127-31","10866298","","",""} kin(p(HGNC:BCR,fus(HGNC:ABL1))) directlyIncreases p(HGNC:CRKL,pmod(P,Y)) kin(p(HGNC:BCR,fus(HGNC:ABL1))) directlyIncreases p(HGNC:GAB2,pmod(P,Y)) """ bcr_abl1_fus = protein_fusion(partner_5p=Protein(namespace='hgnc', name='BCR'), partner_3p=Protein(namespace='hgnc', name='ABL1')) crkl_ph = Protein(namespace='hgnc', name='CRKL', variants=[pmod('Ph', 'Tyr')]) gab2_ph = Protein(namespace='hgnc', name='GAB2', variants=[pmod('Ph', 'Tyr')]) example_graph.add_directly_increases(bcr_abl1_fus, crkl_ph, citation=c5, evidence=e5, annotations={ 'Species': '9606', 'Confidence': 'High' }, subject_modifier=kinase_activity) example_graph.add_directly_increases(bcr_abl1_fus, gab2_ph,