Biology:Bgee
| Bgee gene expression database logo.png | |
|---|---|
| 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 centre | 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 application | Gene search TopAnat: Gene Expression Enrichment Expression comparison Anatomical homology Annotation interface |
| Computer software | bioconductor |
| Miscellaneous | |
| Software license | CC0 1.0 Universal |
| Version | 15.1 |
| Curation policy | Manual 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
- ↑ "Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species". Data Integration in the Life Sciences. Lecture Notes in Computer Science. 5109. 2008. pp. 124–131. doi:10.1007/978-3-540-69828-9_12. ISBN 978-3-540-69827-2.
- ↑ "The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals". Nucleic Acids Research 49 (D1): D831–D847. Jan 2021. doi:10.1093/nar/gkaa793. PMID 33037820.
Further reading
- 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].
- "BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests". F1000Research 5: 2748. 2018. doi:10.12688/f1000research.9973.2. PMID 30467516.
- "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon". J Biomed Semantics 5: 21. 2014. doi:10.1186/2041-1480-5-21. PMID 25009735.
External links
- "Bgee is a new ELIXIR Recommended Interoperability Resources". ELIXIR. 14 December 2023. https://elixir-europe.org/news/resource-announcement-2023.
- "Bgee joins the Global Core Biodata Resources". GCB Global Biodata Coalition. 11 December 2023. https://globalbiodata.org/global-biodata-coalition-announces-outcome-of-2023-global-core-biodata-resource-selection-process/.
- "About Bgee". SIB Swiss Institute of Bioinformatics. 4 January 2021. https://www.sib.swiss/news/from-v1-to-v14-the-gene-expression-database-bgee-under-the-spotlight.
 |  |
