Gene Panels#
The module gene_panels provides functions related to Gene Panels section of
cBioPortal Web Public API.
- pybioportal.gene_panels.fetch_gene_panels(gene_panel_ids, projection='SUMMARY')#
Fetch gene panels from cBioPortal by Gene Panel IDs.
- Parameters:
gene_panel_ids (list of str) – List of Gene Panel IDs.
projection (str) –
Level of detail of the response.
Possible values:
”DETAILED”: Detailed information.
”ID”: Information with only IDs.
”META”: Metadata information.
”SUMMARY”: Summary information (default).
- Returns:
A DataFrame containing the fetched gene panels.
- Return type:
pandas.DataFrame
- pybioportal.gene_panels.get_all_gene_panels(direction='ASC', pageNumber=0, pageSize=10000000, projection='SUMMARY', sortBy=None)#
Get all gene panels from cBioPortal.
- Parameters:
direction (str) –
Direction of the sort.
Possible values:
”ASC”: Ascending (default).
”DESC”: Descending
pageNumber (int) –
Page number of the result list.
Minimum value is 0.
pageSize (int) –
Page size of the result list.
Minimum value is 1, maximum value is 10000000.
projection (str) –
Level of detail of the response.
Possible values:
”DETAILED”: Detailed information.
”ID”: Information with only IDs.
”META”: Metadata information.
”SUMMARY”: Summary information (default).
sortBy – Name of the property that the result list is sorted by.
- Returns:
A DataFrame containing the list of gene panels.
- Return type:
pandas.DataFrame
- pybioportal.gene_panels.get_gene_panel(gene_panel_id)#
Get a specific gene panel from cBioPortal.
- Parameters:
gene_panel_id (str) – Gene Panel ID (e.g., “NSCLC_UNITO_2016_PANEL”).
- Returns:
A DataFrame containing information about the specific gene panel.
- Return type:
pandas.DataFrame
Examples#
from pybioportal import gene_panels as gp
df1 = gp.get_all_gene_panels()
df1.head(10)
| description | genePanelId | |
|---|---|---|
| 0 | Targeted (27 cancer genes) sequencing of adeno... | ACYC_FMI_27 |
| 1 | Targeted panel of 232 genes. | Agilent |
| 2 | Targeted panel of 8 genes. | AmpliSeq |
| 3 | ARCHER-HEME gene panel (199 genes) | ARCHER-HEME-CV1 |
| 4 | ARCHER-SOLID Gene Panel (62 genes) | ARCHER-SOLID-CV1 |
| 5 | Targeted sequencing of various tumor types via... | bait_v3 |
| 6 | Targeted sequencing of various tumor types via... | bait_v4 |
| 7 | Targeted sequencing of various tumor types via... | bait_v5 |
| 8 | Targeted panel of 387 cancer-related genes. | bcc_unige_2016_cancer_panel |
| 9 | Research (CMO) IMPACT-Heme gene panel version 3. | HemePACT_v3 |
df2 = gp.get_gene_panel("NSCLC_UNITO_2016_PANEL")
df2.head(10)
| description | genePanelId | entrezGeneId | hugoGeneSymbol | |
|---|---|---|---|---|
| 0 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 25 | ABL1 |
| 1 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 207 | AKT1 |
| 2 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 324 | APC |
| 3 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 472 | ATM |
| 4 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 673 | BRAF |
| 5 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 999 | CDH1 |
| 6 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 1029 | CDKN2A |
| 7 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 1956 | EGFR |
| 8 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 2064 | ERBB2 |
| 9 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 2066 | ERBB4 |
df3 = gp.fetch_gene_panels(gene_panel_ids=["NSCLC_UNITO_2016_PANEL", "bcc_unige_2016_cancer_panel"],
projection="DETAILED")
df3
| description | genePanelId | entrezGeneId | hugoGeneSymbol | |
|---|---|---|---|---|
| 0 | Targeted panel of 387 cancer-related genes. | bcc_unige_2016_cancer_panel | 25 | ABL1 |
| 1 | Targeted panel of 387 cancer-related genes. | bcc_unige_2016_cancer_panel | 56 | ACRV1 |
| 2 | Targeted panel of 387 cancer-related genes. | bcc_unige_2016_cancer_panel | 2181 | ACSL3 |
| 3 | Targeted panel of 387 cancer-related genes. | bcc_unige_2016_cancer_panel | 91 | ACVR1B |
| 4 | Targeted panel of 387 cancer-related genes. | bcc_unige_2016_cancer_panel | 92 | ACVR2A |
| ... | ... | ... | ... | ... |
| 409 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 4089 | SMAD4 |
| 410 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 6608 | SMO |
| 411 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 6794 | STK11 |
| 412 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 7157 | TP53 |
| 413 | Targeted NGS of NSCLC Samples. | NSCLC_UNITO_2016_PANEL | 7428 | VHL |
414 rows × 4 columns