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,