Release of Bgee version 14.2

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:

• On all gene pages you will now find links to ortholog and paralog gene pages, and links to directly run an expression comparison analysis on them.
• We have made TopAnat faster when used with no decorrelation method.

We have added new RNA-Seq libraries to Bgee. For animals of agronomic and veterinary relevance:

• Bos taurus: 1299 RNA-Seq libraries added
• Sus scrofa: 286 RNA-Seq libraries added
• Cavia porcellus: 255 RNA-Seq libraries added
• Oryctolagus cuniculus: 49 RNA-Seq libraries added
• Canis lupus familiaris: 20 RNA-Seq libraries added
• Equus caballus: 13 RNA-Seq libraries added
• Felis catus : 2 RNA-Seq libraries added

For other species in Bgee:

• Homo sapiens: 47 RNA-Seq libraries added
• Mus musculus: 176 RNA-Seq libraries added
• Macaca mulatta : 22 RNA-Seq libraries added
• Rattus norvegicus: 10 RNA-Seq libraries added
• Monodelphis domestica: 7 RNA-Seq libraries added
• Gorilla gorilla: 2 RNA-Seq libraries added

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:

• We have made changes to the way we propagate expression calls along the graph of conditions: calls of absence of expression are no longer propagated to child anatomical entities, so that an information of absence of expression is more reliable from now on.
• We have also corrected some relations between anatomical entities that were incorrectly missing in our database, improving the propagation of expression calls as well.

• Update of TopAnat:
  • More information is now displayed about the list of genes you entered.
  • It is now possible to use data from any developmental and life stage in a same analysis. Previously, it was only possible to perform analyses for embryonic stage on the one hand, post-embryonic stage on the other hand.
  • Fix various bugs in the interface.
  • Improve queries to the server for faster loading of existing results.
• New publication page listing the publications related to Bgee, and describing how to cite us.
• Fixed several broken links to external resources.

Release of Bgee version 14.1

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.

• For human, 663 RNA-Seq libraries added, 13 removed, for a total of 5,676 libraries in Bgee 14.1; there are now in total 1,794 conditions annotated in Bgee, in 334 anatomical entities.
• For model organisms:
  • 197 libraries added for mouse (total 330 libraries); there are now in total 13,821 conditions annotated in Bgee, in 3,275 anatomical entities.
  • 193 added for Xenopus tropicalis (total 259); 4,808 conditions annotated in Bgee, in 395 anatomical entities.
  • 239 added for Drosophila melanogaster (total 253); 5,704 conditions annotated in Bgee, in 1,138 anatomical entities.
  • 80 added for Danio rerio (total 147); 7,307 conditions annotated in Bgee, in 1,292 anatomical entities.
  • 9 libraries removed for Caenorhabditis elegans (total 41), following improvements of quality controls; 745 conditions annotated in Bgee, in 360 anatomical entities.
• Addition of data also in non-human primates:
  • 235 libraries added for Pan troglodytes (total 250 libraries); there are now in total 70 conditions annotated in Bgee, in 26 anatomical entities.
  • 196 libraries added, 48 removed for Macaca mulatta (total 238); 50 conditions annotated in Bgee, in 25 anatomical entities.
  • 1 library added for Pan paniscus (total 13); 12 conditions annotated in Bgee, in 7 anatomical entities.
• For farm and domestic animals:
  • 224 libraries added for Equus caballus (total 232); there are now in total 58 conditions annotated in Bgee, in 24 anatomical entities.
  • 159 added for Sus scrofa (total 169); 82 conditions annotated in Bgee, in 41 anatomical entities.
  • 135 added for Canis lupus familiaris (total 141); 105 conditions annotated in Bgee, in 54 anatomical entities.
  • 88 added for Bos taurus (total 121); 22 conditions annotated in Bgee, in 19 anatomical entities.
  • 49 added for Oryctolagus cuniculus (total 55); 24 conditions annotated in Bgee, in 19 anatomical entities.
  • 3 added for Gallus gallus (total 48); 30 conditions annotated in Bgee, in 14 anatomical entities.
  • 23 added for Felis catus (total 32); 15 conditions annotated in Bgee, in 11 anatomical entities.
  • 19 added for Cavia porcellus (total 28); 6 conditions annotated in Bgee, in 5 anatomical entities.
• Other species with changes:
  • 89 libraries added for Monodelphis domestica (total 108); there are now in total 51 conditions annotated in Bgee, in 24 anatomical entities.
  • 70 added for Rattus norvegicus (total 106); 64 conditions annotated in Bgee, in 22 anatomical entities.
  • 27 added for Anolis carolinensis (total 31); 20 conditions annotated in Bgee, in 15 anatomical entities.
  • 4 added for Ornithorhynchus anatinus (total 21); 16 conditions annotated in Bgee, in 9 anatomical entities.
  • 2 added, 4 removed for Drosophila simulans (total 15); 7 conditions annotated in Bgee, in 4 anatomical entities.
  • 4 removed for Drosophila pseudoobscura (total 10); 6 conditions annotated in Bgee, in 4 anatomical entities.
• Update of the Expression Comparison page to display expression scores rather than expression ranks.
• Update of the menu, of the collaboration page, of the SPARQL documentation page (notably to access archived version of Bgee, starting with Bgee 14.0).

You can still access Bgee version 14.0 at https://bgee.org/bgee14.

• New score on gene pages.
• New species page.
• Update of the expression comparison.
  • Better sorting approach.
  • Possibility to export results (copy to clipboard or TSV).
• Improve findability of data by adding Bioschemas markup.

• New expression comparison page.
• New anatomical homology page.
• New resource pages: R packages, Annotations, Ontologies and Source code pages.
• New Data dumps and SPARQL endpoint pages.
• New Bgee collaborations page.
• Update of the menu

• Update of the gene search page:
  • Addition of a gene search result page (i.e. search with "HBB")
  • Improvement of the speed of autocompletion
• Modification of gene pages to display gene name synoyms, and cross-references to other resources

• New privacy policy page
• New FAQ page where we address common user queries
• New documentation page specific to GTEx project to learn how we integrated these data into Bgee
• Update to Bgee 14.0 of the gene expression call documentation
• Update of the data source page to provide version information
• We have clarified our license; we have chosen CC0.
• Update of the menu

Release of Bgee version 14.0:

• Release of the production version of Bgee release 14:
  • TopAnat can now be used based on Bgee 14 data.
  • Gene expression calls should now be properly retrieved for all genes.

You can still access Bgee 13 at https://bgee.org/bgee13.

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; inclusion of gene ranks (as used in gene pages) in call files..

You can still access Bgee 13 at https://bgee.org/bgee13.

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.

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).

Various improvements of our new interface.

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.

Major update of TopAnat. Happy Christmas!

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!

Update of the home page.

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.

Release of the multi-species differential expression data (across anatomy) for 6 groups, see download overview.

Release of the single-species differential expression data for 11 species, see download overview.

Release of the single-species expression data for 17 species, see download overview.