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What is Bgee?

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.

Data can be browsed through gene search or expression enrichment analysis. It is also possible to download gene expression calls, processed expression values, or data dumps.

More information is provided in the documentation.

Who are we?

Bgee is developed by the Evolutionary Bioinformatics group, part of the SIB Swiss Institute of Bioinformatics, at the University of Lausanne.

Our main interest is in the evolution of animal genomes in the context of organismal function and development. We have special interests in the early evolution of chordates and fishes. We have the aim of producing a database useful to disciplines such as comparative genomics, Evo-Devo, or transcriptome studies, whilst providing an improved integration of homology and related concepts into bioinformatics through ontologies and ontology tools.

How to cite us?

  • For the use of Bgee:
    Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M.
    Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species.
    in DILS: Data Integration in Life Sciences. Lecture Notes in Computer Science. 5109:124-131. [url] RIS
  • For UBERON:
    Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.
    Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
    in J Biomed Semantics. (2014): 5:21. [url] RIS
  • For the use of the BgeeDB R package:
    Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian F.
    BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests.
    in F1000Research. 2018, 5:2748. [url] RIS

Which license did we choose?

To the extent possible under law, Bgee team has waived all copyright and related or neighboring rights to Bgee project. This work is published under the Creative Commons Zero license (CC0) from Switzerland. Although CC0 doesn’t legally require users of the data to cite the source, if you intend to use data from Bgee, it would be nice to cite us.


Any third party material on this site is the property of its original copyright holders; see notably "information about original images" at the bottom of our homepage for the animal photos copyright.

What is our privacy policy?

You can find all details about our privacy policy in the dedicated page Bgee privacy notice


Our pipeline source code, as well as our curation and ontology resources can be browsed on our GitHub page.

More information about data analyses and database content is available in the documentation.

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