Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species.
It 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 a database for retrieval and comparison of gene expression patterns across multiple animal species, produced from multiple data types (bulk RNA-Seq, single-cell RNA-Seq, Affymetrix, in situ hybridization, and EST data) and from multiple data sets (including GTEx data).
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.
This is a major update of Bgee, with 28 new species; integration of single-cell RNA-Seq full-length data; improved treatment of bulk RNA-Seq, and addition of new libraries; and improved statistical treatment to control for False Discovery Rate. All in situ hybridization data retrieved from Model Organism Databases, and all genomes and underlying ontologies, have been updated.
It is for now released as a beta version. Please note that the data for this beta release will not be archived and should not be used in publications, expecting long-term retrieval. The SPARQL endpoint was not updated.
You can still access Bgee version 14.2 at https://bgee.org/bgee15_0/bgee14_2.
This is an incremental update of Bgee, improving data coverage mostly for animals of agronomic and veterinary relevance, and adding new functionalities to the website:
We have added new RNA-Seq libraries to Bgee. For animals of agronomic and veterinary relevance:
For other species in Bgee:
All calls of presence/absence of expression, expression scores, and all the Bgee tools and download files, have been updated accordingly.
Other changes in this release:
This is an incremental update of Bgee, with an updated RNA-Seq dataset, using the same genomes and ontologies as for the previous version Bgee 14.0. New RNA-Seq libraries have been added; some libraries previously integrated in Bgee have been discarded following corrections and improvements of quality controls. The Affymetrix, in situ hybridization, and EST datasets, are the same as for the previous release of Bgee 14.0. All calls of presence/absence of expression, expression scores, and all the Bgee tools and download files, have been updated accordingly.
For most species in Bgee, notably non-human primates and farm and domestic animals, this represents a major improvement of the anatomy and life stage coverage of the data, making all Bgee tools much more useful, notably TopAnat and the gene pages.
You can still access Bgee version 14.0 at https://bgee.org/bgee15_0/bgee14.
Images from Wikimedia Commons. In most cases, pictures corresponds to the sequenced strains. Show information about original images.
Homo sapiens picture by Leonardo da Vinci (Life time: 1519) [Public domain]. See H. sapiens picture via Wikimedia Commons
Danio rerio picture by Azul (Own work) [see page for license], See D. rerio picture via Wikimedia Commons
Bos taurus picture by User Robert Merkel on en.wikipedia (US Department of Agriculture) [Public domain], See B. taurus picture via Wikimedia Commons
Sus scrofa picture by Joshua Lutz (Own work) [Public domain], See S. scrofa picture via Wikimedia Commons
Equus caballus picture by Doug Antczak Baker Institute for Animal Health College of Veterinary Medicine Cornell University [Public Domain], See E. caballus picture via Wikimedia Commons
Canis lupus familiaris picture by Mood210 (Own work) [CC-BY-SA-3.0], See C. lupus familiaris picture via Wikimedia Commons
Monodelphis domestica picture by Marsupial Genome Sheds Light on the Evolution of Immunity. Hill E, PLoS Biology Vol. 4/3/2006, e75 http://dx.doi.org/10.1371/journal.pbio.0040075 [CC-BY-2.5], See M. domestica picture via Wikimedia Commons
Meleagris gallopavo picture by Riki7 (Own work) [Public domain], See M. gallopavo picture via Wikimedia Commons
Nothobranchius furzeri picture by Ugau (Own work, Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Jena, Germany) [GFDL or CC-BY-SA-3.0], See N. furzeri picture via Wikimedia Commons
Drosophila pseudoobscura picture, See D. pseudoobscura picture via Ensembl Metazoa
Drosophila simulans picture by Nicolas Gompel [CC BY-NC-SA 2.0 FR], See D. simulans picture via Nicolas Gompel's lab website