version 14-beta
Gene expression data in animals

Gene expression data

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data).

Simply normal

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

Comparable between species

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.


Species with data in Bgee(click on species to see more details)
H. sapiens

H. sapiens

human

M. musculus

M. musculus

mouse

D. rerio

D. rerio

zebrafish

D. melanogaster

D. melanogaster

fruit fly

C. elegans

C. elegans

nematode

P. troglodytes

P. troglodytes

chimpanzee

P. paniscus

P. paniscus

bonobo

G. gorilla

G. gorilla

gorilla

M. mulatta

M. mulatta

macaque

R. norvegicus

R. norvegicus

rat

B. taurus

B. taurus

cattle

S. scrofa

S. scrofa

pig

E. caballus

E. caballus

horse

O. cuniculus

O. cuniculus

rabbit

C. lupus familiaris

C. lupus familiaris

dog

F. catus

F. catus

cat

C. porcellus

C. porcellus

guinea pig

E. europaeus

E. europaeus

hedgehog

M. domestica

M. domestica

opossum

O. anatinus

O. anatinus

platypus

G. gallus

G. gallus

chicken

A. carolinensis

A. carolinensis

green anole

X. tropicalis

X. tropicalis

western clawed frog

D. ananassae

D. ananassae

Drosophila ananassae

D. mojavensis

D. mojavensis

Drosophila mojavensis

D. pseudoobscura

D. pseudoobscura

Drosophila pseudoobscura

D. simulans

D. simulans

Drosophila simulans

D. virilis

D. virilis

Drosophila virilis

D. yakuba

D. yakuba

Drosophila yakuba

News (features are being added incrementally)
2017-05-16
Release of Bgee version 14-beta:
  • 12 new species, bringing the total to 29:
    • new mammal species: horse, rabbit, dog, cat, guinea pig, hedgehog;
    • new Drosophila species: D. ananassae, D. mojavensis, D. pseudoobscura, D. simulans, D. virilis, D. yakuba.
  • All species now have RNA-Seq data.
  • Addition of curated human RNA-Seq data from GTEx, removing unhealthy samples; see human data.
  • Improved quality annotation of calls: replacement of "low quality" / "high quality" by:
    • "Gold": ≥2 experiments with a high confidence calls;
    • "Silver": 1 experiment with a high confidence call, or ≥2 experiments with low confidence calls;
    • "Bronze": 1 experiment with a low confidence call; these are not shown by default.
  • Update of download pages to make it easier to chose files to retrieve.
You can still access to Bgee 13 at http://bgee.org/bgee13.
2016-07-06
Release of Bgee version 13.2:
  • Major update of our gene page and ranking algorithm:
    • We are happy to announce that we have updated our ranking algorithm allowing to discover the most relevant anatomical entities and life stages where a gene is expressed. We hope that you will appreciate the noticeable improvements.
    • The gene page has been updated to display the rank scores of conditions where a gene is expressed, allowing to easily identify major functional shifts in gene expression.
    Give a try to this updated ranking by searching for your favorite gene, or by using the example links, on the gene search page.
  • We now display more information about the sources of data used in Bgee, see the new data source page, and new information added to the gene pages.
2016-05-09
Release of our new BgeeDB R package, a package for the annotation and gene expression data download from Bgee database into R, and TopAnat analysis (see also Bioconductor website).
2016-03-22
Various improvements of our new interface.
2016-03-09
Release of our new gene page, allowing to discover the most relevant conditions where a gene is expressed. This update also includes an important revamping of our interfaces.
2015-12-24
Major update of TopAnat. Happy Christmas!
2015-11-24
We are happy to release of our new exclusive tool for gene expression enrichment analyses: TopAnat. This is a tool with absolutely no equivalent, developped in collaboration with the Web-Team of the SIB Swiss Institute of Bioinformatics. Check it out!
2015-08-26
Update of the home page.
2015-06-08
Release of Bgee version 13.1:
  • Update of the website interfaces.
  • New download page providing processed expression values.
  • Addition of mouse in situ data from MGI, see mouse data.
  • Differential expression data have been added for zebrafish, chimpanzee, gorilla, and opossum.
  • Addition of new multi-species differential expression data, see for instance chimpanzee/macaque comparison.
  • New format to provide gene orthology information in multi-species files, see for instance OMA Hierarchical orthologous groups documentation.
  • Removal of data incorrectly considered as normal in C. elegans, see worm data.
  • Improved filtering of propagated no-expression calls. As a result, complete expression calls files do not contain invalid conditions anymore.
  • Filtering of invalid developmental stages for differential expression analyses.
2015-04-16
Release of the multi-species differential expression data (across anatomy) for 6 groups, see download page.
2015-03-03
Release of the single-species differential expression data for 11 species, see download page.
2014-12-19
Release of the single-species expression data for 17 species, see download page.

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

Mus musculus picture by Rasbak [GFDL or CC-BY-SA-3.0], See M. musculus picture via Wikimedia Commons

Danio rerio picture by Azul (Own work) [see page for license], See D. rerio picture via Wikimedia Commons

Drosophila melanogaster picture by André Karwath aka Aka (Own work) [CC-BY-SA-2.5], See D. melanogaster picture via Wikimedia Commons

Caenorhabditis elegans picture by Bob Goldstein, UNC Chapel Hill http://bio.unc.edu/people/faculty/goldstein/ (Own work) [CC-BY-SA-3.0], See C. elegans picture via Wikimedia Commons

Pan troglodytes picture by Thomas Lersch (Own work) [GFDL, CC-BY-SA-3.0 or CC-BY-2.5], See P. troglodytes picture via Wikimedia Commons

Pan paniscus picture by Ltshears (Own work) [CC-BY-SA-3.0 or GFDL], See P. paniscus picture via Wikimedia Commons

Gorilla gorilla picture by Brocken Inaglory (Own work) [CC-BY-SA-3.0 or GFDL], See G. gorilla picture via Wikimedia Commons

Macaca mulatta picture by Aiwok (Own work) [GFDL or CC-BY-SA-3.0-2.5-2.0-1.0], See M. mulatta picture via Wikimedia Commons

Rattus norvegicus picture by Reg Mckenna (originally posted to Flickr as Wild Rat) [CC-BY-2.0], See R. norvegicus 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

Oryctolagus cuniculus picture by JJ Harrison (Own work) [CC-BY-SA-3.0], See O. cuniculus 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

Felis catus picture [CC-BY-SA-3.0], See F. catus picture via Wikimedia Commons

Cavia porcellus picture by Variraptor (Own work) [CC-BY-SA-3.0], See C. porcellus picture via Wikimedia Commons

Erinaceus europaeus picture by Michael Gäbler (Own work) [CC-BY-SA-3.0], See E. europaeus 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

Ornithorhynchus anatinus picture by Dr. Philip Bethge (private) [GFDL or CC-BY-SA-3.0-2.5-2.0-1.0], See O. anatinus picture via Wikimedia Commons

Gallus gallus picture by Subramanya C K (Own work) [CC-BY-SA-3.0], See G. gallus picture via Wikimedia Commons

Anolis carolinensis picture by PiccoloNamek (Moved from Image:P1010027.jpg) [GFDL or CC-BY-SA-3.0], See A. carolinensis picture via Wikimedia Commons

Xenopus tropicalis picture by Václav Gvoždík (http://calphotos.berkeley.edu) [CC-BY-SA-2.5, CC-BY-SA-2.5 or CC-BY-SA-3.0], See X. tropicalis picture via Wikimedia Commons

Drosophila ananassae picture by Nicolas Gompel [CC BY-NC-SA 2.0 FR], See D. ananassae picture via Nicolas Gompel's lab website

Drosophila mojavensis picture by Nicolas Gompel [CC BY-NC-SA 2.0 FR], See D. mojavensis picture via Nicolas Gompel's lab website

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

Drosophila virilis picture by Nicolas Gompel [CC BY-NC-SA 2.0 FR], See D. virilis picture via Nicolas Gompel's lab website

Drosophila yakuba picture by Nicolas Gompel [CC BY-NC-SA 2.0 FR], See D. yakuba picture via Nicolas Gompel's lab website

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