Gene Panel Data#

The module gene_panel_data provides functions related to Gene Panel Data section of cBioPortal Web Public API.

pybioportal.gene_panel_data.fetch_gene_panel_data(molecular_profile_ids=None, molecular_prof_sample_ids=None)#

Fetch gene panel data from cBioPortal.

Parameters:

molecular_profile_ids (list of str) – List of Molecular Profile IDs (e.g., [“brca_tcga_gistic”, “brca_tcga_mutations”, “acc_tcga_gistic”]).
molecular_prof_sample_ids – List of Molecular Profile ID and Sample IDs pairs.

Returns:

A DataFrame containing the fetched gene panel data.

Return type:

pandas.DataFrame

pybioportal.gene_panel_data.fetch_gene_panel_data_in_molecular_profile(molecular_profile_id, sample_ids=None, sample_list_id=None)#

Get gene panel data for a specific molecular profile.

Parameters:

molecular_profile_id (str) – Molecular Profile ID (e.g., “brca_tcga_mutations”).
sample_ids (list of str) – List of Sample IDs (e.g., [“TCGA-AR-A1AR-01”, “TCGA-E2-A1BC-01”] and sample_list_id set to None).
sample_list_id (str) – Sample List ID (e.g., “brca_tcga_all” and sample_ids set to None).

Returns:

A DataFrame containing the fetched gene panel data.

Return type:

pandas.DataFrame

Examples#

from pybioportal import gene_panel_data as gpd

df1a = gpd.fetch_gene_panel_data(molecular_profile_ids=["brca_tcga_gistic", "acc_tcga_gistic", "brca_tcga_mutations"])
df1a

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	profiled
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	brca_tcga	True
1	VENHQS1CSC1BMUVPLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVPOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-BH-A1EO-01	TCGA-BH-A1EO	brca_tcga	True
2	VENHQS1CSC1BMUVTLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVTOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-BH-A1ES-01	TCGA-BH-A1ES	brca_tcga	True
3	VENHQS1CSC1BMUVTLTA2OmJyY2FfdGNnYQ	VENHQS1CSC1BMUVTOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-BH-A1ES-06	TCGA-BH-A1ES	brca_tcga	False
4	VENHQS1CSC1BMUVULTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVUOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-BH-A1ET-01	TCGA-BH-A1ET	brca_tcga	True
...	...	...	...	...	...	...	...
2303	VENHQS1FMi1BMUI0LTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUI0OmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1B4-01	TCGA-E2-A1B4	brca_tcga	True
2304	VENHQS1FMi1BMUI1LTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUI1OmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1B5-01	TCGA-E2-A1B5	brca_tcga	True
2305	VENHQS1FMi1BMUI2LTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUI2OmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1B6-01	TCGA-E2-A1B6	brca_tcga	True
2306	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1BC-01	TCGA-E2-A1BC	brca_tcga	True
2307	VENHQS1FMi1BMUJELTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJEOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1BD-01	TCGA-E2-A1BD	brca_tcga	True

2308 rows × 7 columns

df1b = gpd.fetch_gene_panel_data(molecular_prof_sample_ids=[
                                            {"molecular_profile_id": "brca_tcga_gistic",
                                             "sample_ids": ["TCGA-AR-A1AR-01", "TCGA-E2-A1BC-01"]},
                                            {"molecular_profile_id": "brca_tcga_mutations",
                                             "sample_ids": ["TCGA-AR-A1AR-01", "TCGA-E2-A1BC-01"]},
                                            {"molecular_profile_id": "msk_met_2021_mutations",
                                             "sample_ids": ["P-0000004-T01-IM3", "P-0000950-T01-IM3"]}
                                  ])
df1b

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	profiled	genePanelId
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	brca_tcga	True	NaN
1	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	brca_tcga	True	NaN
2	UC0wMDAwMDA0LVQwMS1JTTM6bXNrX21ldF8yMDIx	UC0wMDAwMDA0Om1za19tZXRfMjAyMQ	msk_met_2021_mutations	P-0000004-T01-IM3	P-0000004	msk_met_2021	True	IMPACT341
3	UC0wMDAwOTUwLVQwMS1JTTM6bXNrX21ldF8yMDIx	UC0wMDAwOTUwOm1za19tZXRfMjAyMQ	msk_met_2021_mutations	P-0000950-T01-IM3	P-0000950	msk_met_2021	True	IMPACT341
4	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-AR-A1AR-01	TCGA-AR-A1AR	brca_tcga	True	NaN
5	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1BC-01	TCGA-E2-A1BC	brca_tcga	True	NaN

df2a = gpd.fetch_gene_panel_data_in_molecular_profile("brca_tcga_mutations",sample_ids=["TCGA-AR-A1AR-01", "TCGA-E2-A1BC-01"])
df2a

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	profiled
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-AR-A1AR-01	TCGA-AR-A1AR	brca_tcga	True
1	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A1BC-01	TCGA-E2-A1BC	brca_tcga	True

df2b = gpd.fetch_gene_panel_data_in_molecular_profile("brca_tcga_mutations", sample_list_id="brca_tcga_all")
df2b

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	studyId	profiled
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-AR-A1AR-01	TCGA-AR-A1AR	brca_tcga	True
1	VENHQS1CSC1BMUVPLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVPOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-BH-A1EO-01	TCGA-BH-A1EO	brca_tcga	True
2	VENHQS1CSC1BMUVTLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVTOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-BH-A1ES-01	TCGA-BH-A1ES	brca_tcga	True
3	VENHQS1CSC1BMUVULTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVUOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-BH-A1ET-01	TCGA-BH-A1ET	brca_tcga	True
4	VENHQS1CSC1BMUVVLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMUVVOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-BH-A1EU-01	TCGA-BH-A1EU	brca_tcga	True
...	...	...	...	...	...	...	...
1103	VENHQS1FMi1BMTVBLTA2OmJyY2FfdGNnYQ	VENHQS1FMi1BMTVBOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A15A-06	TCGA-E2-A15A	brca_tcga	True
1104	VENHQS1CSC1BMThWLTA2OmJyY2FfdGNnYQ	VENHQS1CSC1BMThWOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-BH-A18V-06	TCGA-BH-A18V	brca_tcga	True
1105	VENHQS1FMi1BMTVLLTA2OmJyY2FfdGNnYQ	VENHQS1FMi1BMTVLOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A15K-06	TCGA-E2-A15K	brca_tcga	True
1106	VENHQS1FMi1BMTVFLTA2OmJyY2FfdGNnYQ	VENHQS1FMi1BMTVFOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-E2-A15E-06	TCGA-E2-A15E	brca_tcga	True
1107	VENHQS1BQy1BNklYLTA2OmJyY2FfdGNnYQ	VENHQS1BQy1BNklYOmJyY2FfdGNnYQ	brca_tcga_mutations	TCGA-AC-A6IX-06	TCGA-AC-A6IX	brca_tcga	False

1108 rows × 7 columns