Bgee
Bgee gene expression database logo
Content
DescriptionGene expression across species and conditions
Data types
captured		scRNA-Seq, RNA-Seq, Microarray, In situ and EST Data
OrganismsHuman, Mouse, Rat, Fruit-fly, Chicken, Roundworm, Wild boar, Zebrafish, Cow and others.
Contact
Research centerSwiss Institute of Bioinformatics
University of Lausanne
Primary citationPMID 33037820
Release dateJune 2007
Access
Websitewww.bgee.org
Download URLwww.bgee.org
Sparql endpointwww.bgee.org/sparql/
Tools
WebGene search
TopAnat: Gene Expression Enrichment
Expression comparison
Anatomical homology
Annotation interface
Standalonebioconductor.org/packages/BgeeDB/ bioconductor.org/packages/BgeeCall/
Miscellaneous
LicenseCC0 1.0 Universal
Version15.1
Curation policyManual curation of every study.

Bgee is a database maintained by the SIB Swiss Institute of Bioinformatics and the University of Lausanne for retrieval and comparison of gene expression patterns from RNA-Seq, scRNA-Seq, Microarray, In situ hybridization and EST studies, across multiple animal species.[1][2] Bgee provides an intuitive answer to the question where is a gene expressed? and supports research in cancer and agriculture, as well as evolutionary biology.

Bgee is based exclusively on curated, healthy wild-type, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of healthy wild-type 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.

Bgee allows searches by gene, organs / tissue / cell type and developmental stage.

Bgee is a part of Global Core Biodata Resources (GCBRs) representing "critical components for ensuring the reproducibility and integrity of life sciences research." Bgee is also an ELIXIR Recommended Interoperability Resources that facilitate the FAIR-supporting activities in scientific research.

References

  1. ↑ Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M (2008). "Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species". Data Integration in the Life Sciences. Lecture Notes in Computer Science. Vol. 5109. pp. 124–131. doi:10.1007/978-3-540-69828-9_12. ISBN 978-3-540-69827-2.
  2. ↑ Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, Mendes de Farias T, et al. (Jan 2021). "The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals". Nucleic Acids Research. 49 (D1): D831–D847. doi:10.1093/nar/gkaa793. PMC 7778977. PMID 33037820.

Further reading

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