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{{infobox biodatabase |
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#REDIRECT [[Baldur's Gate: Enhanced Edition]] |
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|logo = [[File:Bgee gene expression database logo.png|thumb|Bgee gene expression database logo]] |
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|title = '''Bgee''' |
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|description = Gene expression across species and conditions |
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|scope = scRNA-Seq, RNA-Seq, Microarray, In situ and EST Data |
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|organism = Human, Mouse, Rat, Fruit-fly, Chicken, Roundworm, Wild boar, Zebrafish, Cow and others. |
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|center = [[Swiss Institute of Bioinformatics]]<br>[[University of Lausanne]] |
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|pmid = 33037820 |
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|released = June 2007 |
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|url = {{URL|https://www.bgee.org}} |
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|download = {{URL|https://www.bgee.org}} |
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|sparql = {{URL|https://www.bgee.org/sparql/}} |
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|webapp = [https://www.bgee.org/search/genes Gene search]<br>[https://www.bgee.org/analysis/top-anat/ TopAnat: Gene Expression Enrichment]<br>[https://www.bgee.org/analysis/expr-comparison Expression comparison]<br>[https://www.bgee.org/search/anatomical-homology Anatomical homology]<br>[https://annotations.bgee.org Annotation interface] |
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|standalone = {{URL|https://bioconductor.org/packages/BgeeDB/}} {{URL|https://bioconductor.org/packages/BgeeCall/}} |
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|curation = Manual curation of every study. |
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|bookmark = |
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|license = [https://creativecommons.org/publicdomain/zero/1.0/ CC0 1.0 Universal] |
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|version = 15.0 |
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}} |
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'''Bgee''' is a [[biological database|database]] maintained by the [[Swiss Institute of Bioinformatics]] and the [[University of Lausanne]] for retrieval and comparison of [[gene expression]] patterns from [[RNA-Seq]], [[scRNA-Seq]], [[DNA_microarray|Microarray]], [[In situ hybridization]] and [[Expressed sequence tag|EST]] studies, across multiple [[animal]] [[species]].<ref>{{cite journal | vauthors = Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M | title = Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species | journal = Lecture Notes in Computer Science | volume = 5109 | pages = 124-131 | date = 2008 | doi = 10.1007/978-3-540-69828-9_12 }}</ref><ref>{{cite journal | vauthors = Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, Mendes de Farias T, Moretti S, Parmentier G, Rech de Laval V, Rosikiewicz M, Wollbrett J, Echchiki A, Escoriza A, Gharib W, Gonzales-Porta M, Jarosz Y, Laurenczy B, Moret P, Person E, Roelli P, Sanjeev K, Seppey M, Robinson-Rechavi M | display-authors = 6 | title = The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals | journal = Nucleic Acids Research | volume = 49 | issue = D1 | pages = D831-D847 | date = Jan 2021 | pmid = 33037820 | doi = 10.1093/nar/gkaa793 | pmc = 7778977 | doi-access = free }}</ref> 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]]. |
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Bgee is based exclusively on curated '''normal''', '''healthy [[Wild type|wild-type]]''', expression data (e.g., no [[Gene knockout|gene knock-out]], no treatment, no [[disease]]), to provide a comparable reference of normal gene expression. |
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Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene [[Sequence homology#Orthology|orthology]], and of [[Homology (biology)|homology]] between [[Organ (biology)|organs]]. This allows comparisons of expression patterns between [[species]]. |
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Bgee allows searches by [[gene]], [[Organ (biology)|organs]] / [[Tissue (biology)|tissue]] / [[cell type]] and [[Developmental biology|developmental stage]]. |
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== References == |
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{{reflist}} |
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== Further reading == |
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{{refbegin}} |
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* {{cite journal | vauthors = Niknejad A, Mungall CJ, Osumi-Sutherland D, Robinson-Rechavi M, Bastian F | title = Creation and unification of development and life stage ontologies for animals | journal = arXiv | date = 2022 | doi = 10.48550/arXiv.2206.12231 | doi-access = free }} |
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* {{cite journal | vauthors = Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian F | title = BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests | journal = F1000Research | volume = 5 | pages = 2748 | date = 2018 | pmid = 30467516 | doi = 10.12688/f1000research.9973.2 | pmc = 6113886 | doi-access = free }} |
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* {{cite journal | vauthors = 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 | display-authors = 6 | title = Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon | journal = J Biomed Semantics | volume = 5 | pages = 21 | date = 2014 | pmid = 25009735 | doi = 10.1186/2041-1480-5-21 | pmc = 4089931 | doi-access = free }} |
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{{refend}} |
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== External links == |
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* {{cite web | title = About Bgee | url = https://www.sib.swiss/news/from-v1-to-v14-the-gene-expression-database-bgee-under-the-spotlight | publisher = SIB Swiss Institute of Bioinformatics }} |
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[[Category:Genetics databases]] |
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[[Category:Genomics]] |
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[[Category:Open science]] |
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[[Category:Ontology]] |
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[[Category:Evolutionary developmental biology]] |
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[[Category:Subfields of evolutionary biology]] |
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[[Category:Developmental biology]] |
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[[Category:Science and technology in Switzerland]] |
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Revision as of 07:23, 21 November 2023
 | |
| 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 Annotation interface |
| Standalone | bioconductor |
| Miscellaneous | |
| License | CC0 1.0 Universal |
| Version | 15.0 |
| Curation policy | Manual curation of every study. |
Bgee is a database maintained by the 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 normal, healthy wild-type, 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.
Bgee allows searches by gene, organs / tissue / cell type and developmental stage.
References
- ^ Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M (2008). "Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species". Lecture Notes in Computer Science. 5109: 124–131. doi:10.1007/978-3-540-69828-9_12.
- ^ 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
- 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. doi:10.48550/arXiv.2206.12231.
- 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
- "About Bgee". SIB Swiss Institute of Bioinformatics.