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 gene expression database logo | |
| Content | |
|---|---|
| Description | Gene expression across species and conditions |
| Data types captured | scRNA-Seq, RNA-Seq, Microarray, In situ and EST Data |
| Organisms | Human, Mouse, Rat, Fruit-fly, Chicken, Roundworm, Wild boar, Zebrafish, Cow and others. |
| Contact | |
| Research center | Swiss Institute of Bioinformatics University of Lausanne |
| Primary citation | PMID 33037820 |
| Release date | June 2007 |
| Access | |
| Website | www |
| Download URL | www |
| Sparql endpoint | www |
| Tools | |
| Web | Gene search TopAnat: Gene Expression Enrichment Expression comparison Anatomical homology Raw data interface |
| Standalone | bioconductor |
| Miscellaneous | |
| License | CC0 1.0 Universal |
| Version | 15.2 |
| Curation policy | Manual curation of every study. |
Bgee is based exclusively on curated, healthy wild-type, expression data (i.e., 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, organ / 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
edit- ^ 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.
- ^ 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
edit- Niknejad A, Mungall CJ, Osumi-Sutherland D, Robinson-Rechavi M, Bastian F (2022). "Creation and unification of development and life stage ontologies for animals". arXiv:2206.12231 [q-bio.QM].
- Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian F (2018). "BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests". F1000Research. 5: 2748. doi:10.12688/f1000research.9973.2. PMC 6113886. PMID 30467516.
- Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, et al. (2014). "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon". J Biomed Semantics. 5: 21. doi:10.1186/2041-1480-5-21. PMC 4089931. PMID 25009735.
External links
edit- "Bgee is a new ELIXIR Recommended Interoperability Resources". ELIXIR. 14 December 2023.
- "Bgee joins the Global Core Biodata Resources". GCB Global Biodata Coalition. 11 December 2023.
- "About Bgee". SIB Swiss Institute of Bioinformatics. 4 January 2021.