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, expression enrichment analysis, or data download.

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, Robinson-Rechavi M and Bastian F.
    BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests.
    in F1000Research. .[url] RIS


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.