Python arguments are equivalent to long-option arguments (--arg), unless otherwise specified. Flags are True/False arguments in Python. The manual for any gget tool can be called from the command-line using the -h --help flag.

gget bgee 🐝

Fetch orthology and gene expression data from Bgee using Ensembl IDs.
Return format: JSON/CSV (command-line) or data frame (Python).

If you are specifically interested in human gene expression data, consider using gget opentargets or gget archs4 instead. gget bgee has less data, but supports more species.

This module was written by Sam Wagenaar.

Positional argument
ens_id
Ensembl gene ID, e.g. ENSG00000169194 or ENSSSCG00000014725.

NOTE: Some of the species in Bgee are not in Ensembl or Ensembl metazoa, and for those you can use NCBI gene IDs, e.g. 118215821 (a gene in Anguilla anguilla).

Required arguments
-t --type
Type of data to fetch. Options: orthologs, expression.

Optional arguments
-o --out
Path to the JSON file the results will be saved in, e.g. path/to/directory/results.json. Default: Standard out.

Flags
-csv --csv
Command-line only. Returns the output in CSV format, instead of JSON format.
Python: Use json=True to return output in JSON format.

-q --quiet
Command-line only. Prevents progress information from being displayed.
Python: Use verbose=False to prevent progress information from being displayed.

Examples

Get orthologs for a gene

gget bgee ENSSSCG00000014725 -t orthologs

import gget
gget.bgee("ENSSSCG00000014725", type="orthologs")

→ Returns orthologs for the gene with Ensembl ID ENSSSCG00000014725.

gene_id	gene_name	species_id	genus	species
734881	hbb1	8355	Xenopus	laevis
ENSFCAG00000038029	LOC101098159	9685	Felis	catus
ENSBTAG00000047356	LOC107131172	9913	Bos	taurus
ENSOARG00000019163	LOC101105437	9940	Ovis	aries
ENSXETG00000025667	hbg1	8364	Xenopus	tropicalis
...	...	...	...	...

Get gene expression data for a gene

gget bgee ENSSSCG00000014725 -t expression

import gget
gget.bgee("ENSSSCG00000014725", type="expression")

→ Returns gene expression data for the gene with Ensembl ID ENSSSCG00000014725.

anat_entity_id	anat_entity_name	score	score_confidence	expression_state
UBERON:0000178	blood	99.98	high	expressed
UBERON:0002106	spleen	99.96	high	expressed
UBERON:0002190	subcutaneous adipose tissue	99.70	high	expressed
UBERON:0005316	endocardial endothelium	99.61	high	expressed
UBERON:0002107	liver	99.27	high	expressed
...	...	...	...	...

More examples

References

If you use gget bgee in a publication, please cite the following articles:

Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836
Frederic B Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angélique Escoriza, Walid H Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi (2021). The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D831–D847, https://doi.org/10.1093/nar/gkaa793