Basic Usage¶
[1]:
import stringdb
[2]:
genes = ['TP53', 'BRCA1', 'FANCD1', 'FANCL']
string_ids = stringdb.get_string_ids(genes)
string_ids
[2]:
| queryItem | queryIndex | stringId | ncbiTaxonId | taxonName | preferredName | annotation | |
|---|---|---|---|---|---|---|---|
| 0 | TP53 | 0 | 9606.ENSP00000269305 | 9606 | Homo sapiens | TP53 | Cellular tumor antigen p53; Acts as a tumor su... |
| 1 | BRCA1 | 1 | 9606.ENSP00000418960 | 9606 | Homo sapiens | BRCA1 | Breast cancer type 1 susceptibility protein; E... |
| 2 | FANCD1 | 2 | 9606.ENSP00000369497 | 9606 | Homo sapiens | BRCA2 | Breast cancer type 2 susceptibility protein; I... |
| 3 | FANCL | 3 | 9606.ENSP00000385021 | 9606 | Homo sapiens | FANCL | E3 ubiquitin-protein ligase FANCL; Ubiquitin l... |
[3]:
enrichment_df = stringdb.get_enrichment(string_ids.queryItem)
enrichment_df.sort_values('fdr')
[3]:
| category | term | number_of_genes | number_of_genes_in_background | ncbiTaxonId | inputGenes | preferredNames | p_value | fdr | description | |
|---|---|---|---|---|---|---|---|---|---|---|
| 64 | PMID | PMID.22918243 | 4 | 8 | 9606 | TP53,FANCD1,FANCL,BRCA1 | TP53,BRCA2,FANCL,BRCA1 | 8.100000e-14 | 1.160000e-08 | (2012) Switch of FANCL, a key FA-BRCA componen... |
| 106 | PMID | PMID.26842001 | 4 | 12 | 9606 | TP53,FANCD1,FANCL,BRCA1 | TP53,BRCA2,FANCL,BRCA1 | 2.980000e-13 | 2.140000e-08 | (2016) Fanconi anemia genes in lung adenocarci... |
| 127 | PMID | PMID.28423363 | 4 | 22 | 9606 | TP53,FANCD1,FANCL,BRCA1 | TP53,BRCA2,FANCL,BRCA1 | 2.450000e-12 | 2.390000e-08 | (2017) Multiple-gene panel analysis in a case ... |
| 126 | PMID | PMID.28387924 | 4 | 15 | 9606 | TP53,FANCD1,FANCL,BRCA1 | TP53,BRCA2,FANCL,BRCA1 | 6.340000e-13 | 2.390000e-08 | (2017) High number of kinome-mutations in non-... |
| 79 | PMID | PMID.24439051 | 4 | 21 | 9606 | TP53,FANCD1,FANCL,BRCA1 | TP53,BRCA2,FANCL,BRCA1 | 2.070000e-12 | 2.390000e-08 | (2014) Poly(ADP-ribose) polymerase inhibitor C... |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 12 | InterPro | IPR013083 | 2 | 441 | 9606 | FANCL,BRCA1 | FANCL,BRCA1 | 3.000000e-03 | 4.170000e-02 | Zinc finger, RING/FYVE/PHD-type |
| 150 | Process | GO.0008285 | 2 | 669 | 9606 | TP53,FANCD1 | TP53,BRCA2 | 6.700000e-03 | 4.210000e-02 | negative regulation of cell population prolife... |
| 149 | Process | GO.0008283 | 2 | 676 | 9606 | TP53,FANCD1 | TP53,BRCA2 | 6.900000e-03 | 4.260000e-02 | cell population proliferation |
| 141 | Process | GO.0006325 | 2 | 683 | 9606 | TP53,FANCD1 | TP53,BRCA2 | 7.000000e-03 | 4.310000e-02 | chromatin organization |
| 22 | Keyword | KW-0007 | 3 | 3335 | 9606 | TP53,FANCL,BRCA1 | TP53,FANCL,BRCA1 | 1.730000e-02 | 4.760000e-02 | Acetylation |
195 rows × 10 columns
There are 5 functions for querying a list of stringIds, which follow the patter get_*
* can be ‘enrichment’, ‘interaction_partners’, ‘ppi_enrichment’, ‘network’, and ‘functional_annotation’
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