def test_get_ccle_mrna():
mrna = cbio_client.get_ccle_mrna(['XYZ', 'MAP2K1'], ['A375_SKIN'])
assert('A375_SKIN' in mrna)
assert(mrna['A375_SKIN'] is not None)
assert(mrna['A375_SKIN']['MAP2K1'] > 10)
assert(mrna['A375_SKIN']['XYZ'] is None)
mrna = cbio_client.get_ccle_mrna(['EGFR', 'BRAF'], ['XXX'])
assert('XXX' in mrna)
assert(mrna['XXX'] is None)
def test_get_ccle_mrna():
mrna = cbio_client.get_ccle_mrna(['XYZ', 'MAP2K1'], ['A375_SKIN'])
assert 'A375_SKIN' in mrna
assert mrna['A375_SKIN'] is not None
assert mrna['A375_SKIN']['MAP2K1'] > 10
assert mrna['A375_SKIN']['XYZ'] is None
mrna = cbio_client.get_ccle_mrna(['EGFR', 'BRAF'], ['XXX'])
assert 'XXX' in mrna
assert mrna['XXX'] is None
def get_protein_expression(gene_names, cell_types):
"""Return the protein expression levels of genes in cell types.
Parameters
----------
gene_names : list
HGNC gene symbols for which expression levels are queried.
cell_types : list
List of cell type names in which expression levels are queried.
The cell type names follow the CCLE database conventions.
Example: LOXIMVI_SKIN, BT20_BREAST
Returns
-------
res : dict[dict[float]]
A dictionary keyed by cell line, which contains another dictionary
that is keyed by gene name, with estimated protein amounts as values.
"""
A = 0.2438361
B = 3.0957627
mrna_amounts = cbio_client.get_ccle_mrna(gene_names, cell_types)
protein_amounts = copy(mrna_amounts)
for cell_type in cell_types:
amounts = mrna_amounts.get(cell_type)
if amounts is None:
continue
for gene_name, amount in amounts.items():
if amount is not None:
protein_amount = 10**(A * amount + B)
protein_amounts[cell_type][gene_name] = protein_amount
return protein_amounts
def get_protein_expression(gene_names, cell_types):
"""Return the protein expression levels of genes in cell types.
Parameters
----------
gene_names : list
HGNC gene symbols for which expression levels are queried.
cell_types : list
List of cell type names in which expression levels are queried.
The cell type names follow the CCLE database conventions.
Example: LOXIMVI_SKIN, BT20_BREAST
Returns
-------
res : dict[dict[float]]
A dictionary keyed by cell line, which contains another dictionary
that is keyed by gene name, with estimated protein amounts as values.
"""
A = 0.2438361
B = 3.0957627
mrna_amounts = cbio_client.get_ccle_mrna(gene_names, cell_types)
protein_amounts = copy(mrna_amounts)
for cell_type in cell_types:
amounts = mrna_amounts.get(cell_type)
if amounts is None:
continue
for gene_name, amount in amounts.items():
if amount is not None:
protein_amount = 10**(A * amount + B)
protein_amounts[cell_type][gene_name] = protein_amount
return protein_amounts
def get_ccle_mrna_levels():
"""Get CCLE mRNA amounts using cBioClient"""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
gene_list = body.get('gene_list')
cell_lines = body.get('cell_lines')
mrna_amounts = cbio_client.get_ccle_mrna(gene_list, cell_lines)
res = {'mrna_amounts': mrna_amounts}
return res
def get_ccle_mrna_levels():
"""Get CCLE mRNA amounts using cBioClient"""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
gene_list = body.get('gene_list')
cell_lines = body.get('cell_lines')
mrna_amounts = cbio_client.get_ccle_mrna(gene_list, cell_lines)
res = {'mrna_amounts': mrna_amounts}
return res
def contextualize_stmts(stmts, cell_line, genes):
"""Contextualize model at the level of INDRA Statements."""
to_remove = []
cell_line_ccle = cell_line + '_SKIN'
# Remove genes with CNA = -2
print('Contextualize by CNA')
cna = cbio_client.get_ccle_cna(genes, [cell_line_ccle])[cell_line_ccle]
for gene in genes:
if cna.get(gene) == -2:
to_remove.append(gene)
print('To remove CNA: %s' % gene)
# Remove genes with transcripts in bottom 5%
print('Contextualize by mRNA')
mrna = cbio_client.get_ccle_mrna(genes, [cell_line_ccle])[cell_line_ccle]
mrna_vals = [v for v in mrna.values() if v]
if mrna_vals:
thresh = numpy.percentile(mrna_vals, 5.0)
for gene, val in mrna.items():
if val and val < thresh:
to_remove.append(gene)
print('To remove mRNA: %s' % gene)
# Remove genes with nonsense mutations
print('Contextualize by nonsense mutations')
variants = read_ccle_variants(genes)
to_remove_nonsense = list(variants['nonsense'][cell_line_ccle].keys())
if to_remove_nonsense:
print('To remove nonsense: %s' % ', '.join(to_remove_nonsense))
to_remove += to_remove_nonsense
# Remove Statements for these genes
new_stmts = []
for stmt in stmts:
any_to_remove = False
for agent in stmt.agent_list():
if agent is not None and agent.name in to_remove:
any_to_remove = True
break
if not any_to_remove:
new_stmts.append(stmt)
# Remove Statements with irrelevant mutations
print('Contextualize by missense mutations')
mutations = variants['missense'][cell_line_ccle]
muts_to_use = {}
for gene, mut_list in mutations.items():
muts_to_use[gene] = []
for mut in mut_list:
muts_to_use[gene].append(mut)
stmts = ac.filter_mutation_status(new_stmts, mutations, [])
return stmts
def analyze_cna_mrna(genes, cell_line):
"""Plot CNA vs mRNA reported by CCLE for given genes in a cell line."""
import matplotlib.pyplot as plt
cna = cbio_client.get_ccle_cna(genes, [cell_line])[cell_line]
mrna = cbio_client.get_ccle_mrna(genes, [cell_line])[cell_line]
plt.ion()
plt.figure()
for gene, cna_val in cna.items():
if cna_val is None or gene not in mrna:
continue
mrna_val = mrna[gene]
if mrna_val is None:
continue
plt.plot(cna_val, mrna_val, 'ro', alpha=0.5)
plt.xlim([-2.1, 2.1])
cna_vals = list(range(-2, 3))
plt.title('%s cell line' % cell_line)
plt.xticks(cna_vals, [str(c) for c in cna_vals])
plt.ylabel('mRNA amounts reported by CCLE')
plt.xlabel('DNA copy number alteration reported by CCLE')
plt.show()
def post(self):
"""Get CCLE mRNA amounts using cBioClient
Parameters
----------
gene_list : list[str]
A list of HGNC gene symbols to get mRNA amounts for.
cell_lines : list[str]
A list of CCLE cell line names to get mRNA amounts for.
Returns
-------
mrna_amounts : dict[dict[float]]
A dict keyed to cell lines containing a dict keyed to genes
containing float
"""
args = request.json
gene_list = args.get('gene_list')
cell_lines = args.get('cell_lines')
mrna_amounts = cbio_client.get_ccle_mrna(gene_list, cell_lines)
res = {'mrna_amounts': mrna_amounts}
return res
