News

2024-05-21

Release of Bgee version 15.2

In this release, we have added hundreds of curated, standardized, and processed single-cell 10X Genomics libraries. You can retrieve them from our raw data interface.

We have also added about 14,000 bulk RNA-Seq libraries to allow for more meaningful gene expression comparisons across species. We targeted specific organs and species for which comparisons were not yet possible.

Of note, these new data are not yet fully integrated in our tools such as the gene expression pages and TopAnat. Thanks to this partial update, we are now able to respond quickly to the need for curation and standardization of new datasets. The full integration of these data in our tools and gene expression pages will be included in the following release.

This release includes the addition of a large number of bulk RNA-Seq libraries in Salmo salar (Atlantic salmon). We also now provide "physiological status", which holds information about the smoltification status of individuals, which is especially relevant for Salmo salar. These new data have been fully integrated in all our tools and gene expression pages, as opposed to the new data added in other species (see point above).

We also provide new information for annotated samples in this release: you can now retrieve free text information provided by the authors, along with the standardized ontology terms to capture information about anatomy, cell type, developmental and life stage. This is especially useful for single-cell RNA-Seq data, where the ontologies are not always able to capture the diversity of cell types identified in such experiments.

2024-01-03

Bgee becomes a GCBR and Elixir Interoperability service

We are happy to announce that Bgee has been selected as a Global Core Biodata Resource by the Global Biodata Coalition. It means that the GBC panel of independent experts considers Bgee as a resource of fundamental importance to the life science community. We are very pleased that our contribution is recognized in data curation and standardization, ontology development, and in creating new knowledge from gene expression data. Bgee joins the list of 52 GCBRs as of today.

Moreover, Bgee has been recognized as a Recommended Interoperability Resource by Elixir. The Elixir panel of external experts identifies Bgee as a resource contributing to FAIR data access in life science.

This is of course great news for us, but more importantly should allow us in the future to better support our activities, in order to continue providing effective access to reusable gene expression data, and develop new tools to support your research activities.

2023-11-14

Release of Bgee version 15.1

This release rolls out the integration in Bgee of droplet-based single-cell RNA-Seq data (e.g., 10x Genomics data), after the integration of full-length single-cell data in the previous release (e.g., Smart-Seq data).

We have focused on updating Drosophila melanogaster data, with the integration of the Fly Cell Atlas (FCA), and 3 other single-cell experiments. The methods established in this release will enable us to integrate many more droplet-based data for any species in Bgee in future updates.

As with all other data in Bgee, we have reannotated and integrated single-cell data to make them comparable between other species and datasets:

  • For instance, while the Fly Cell Atlas has been originally annotated with fly-specific vocabularies (i.e., FBbt ontology), Bgee reconnects these data to species-neutral terms (i.e., from Uberon and CL ontologies) to enhance comparisons between species, while still conserving precise fly-specific terms when necessary.
  • Droplet-based data are fully integrated in our expression calls and expression scores as any other data type. See for instance the expression calls for the fly gene eya ("Developmental protein eyes absent"), where expression in, e.g., "visual pigment cell" from single cell data, is integrated along with expression in, e.g., "visual primordium" from in situ hybridization data. To do so, we use a pseudobulk approach per cell type and library to have enough signal to reliably characterize gene expression in cell populations.
  • You can in any case obtain annotations and gene read counts per each cell in H5AD format for droplet-based experiments, see for instance the experiment page dedicated to the Fly Cell Atlas, button "Download all assays". For full length experiments (e.g., Smart-Seq data), we still provide this information in TSV format, where each file contains the data for one cell, see for instance this Smart-Seq experiment in human.

You can browse all experiments annotated and integrated in Bgee on our raw data search page, notably, scRNA-Seq experiments.

2023-04-24

New interface which provides access to all of our detailed annotations and calls of expression:

  • The Raw data annotations page allows to browse and select the annotations of bulk RNA-seq, single-cell RNA-seq, microarrays, ESTs and in situ hybridization. For each experiment we provide detailed annotations and corresponding processed expression values (e.g., TPM, read count, p-value of expression call). All experiments are linked to source databases.
  • The Expression calls page allows to browse and export all present/absent expression calls in Bgee, per species, gene, and condition.
  • Both Raw data and Expression calls can be filtered by species, anatomy, cell type, development and life stage, sex and strain/ethnicity.
  • Each experiment integrated in Bgee now has a dedicated page, where annotations and processed expression values can be browsed and downloaded. See for instance the GTEx experiment page

We have also added the following pages:

Bgee is on Mastodon

2023-03-31

Our SIB course "Gene Expression made Useful Easily: Tools and Database of Bgee" is open for registration:

  • Online (streamed) course on 26 May, registration till 12 May
  • Morning: lectures
    • Bgee, biocuration, calls of expression, data integration, and bioinformatics tools
  • Afternoon: 2 parallel hands-on sessions, each ½ web ½ RStats
    • Accessing curated transcriptome data
    • Bgee tools: making gene expression useful

Course information and registration

--

We are recruiting a postdoc to work on the bioinformatics / biostatistics of new types of gene expression data in Bgee: new single-cell, isoform-specific RNA-seq, etc. We integrate all data types into summary scores and calls of expression, so there are a lot of challenges in integrating each new data type. And a lot of opportunities both for methodological research, and for downstream biology using these newly integrated data.

Postdoctoral position details and application

2022-03-29

Release of Bgee version 15.0

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.

The frontend used to access Bgee has also been completely updated to use a React framework.

  • We are happy to announce that Bgee now includes single-cell RNA-Seq full-length data. We have designed statistical methods allowing to produce reliable present expression calls and expression scores for this data type. We also use annotation procedures allowing to capture with a high precision the cell types studied and their anatomical origin (post-composition of ontology terms). It is straightforwardly integrated in all our tools, along with all other data (bulk RNA-Seq, Affymetrix, in situ hybridization, Expressed Sequence Tags). For this release, we have integrated 1 481 libraries in human and mouse.

  • 28 species have been added, while 5 species have been discontinued, due to new criteria on anatomical coverage. In total, Bgee now integrates expression data in 52 species.

  • We have improved the control of False Discovery Rate to produce present/absent expression calls. Rather than integrating boolean calls (where present calls always dominate), we produce a p-value for each expression call from each sample, and integrate these to produce a single call for each gene in each condition, using a Benjamini-Hochberg procedure to control for FDR.

  • We have improved the treatment of bulk RNA-Seq data to generate more reliable absent expression calls. We now annotate precisely the protocol used to generate libraries (e.g., polyA, ribo-minus), and the gene types targeted (e.g., protein coding, miRNA). With this information, we produce absent expression calls for a gene only if its type was accessible to the RNA-Seq protocol used.

  • Bgee 15.0 includes 4 965 more bulk RNA-Seq libraries, for a total of 15 516. 5 793 bulk RNA-Seq libraries have been added, and 802 libraries removed following improved quality controls.

    • For model organisms:
      • 252 added for Homo sapiens (total library count: 5 975)
      • 73 added, 13 removed for Mus musculus (total: 566)
      • 14 added for Danio rerio (total: 161)
      • 4 added for Drosophila melanogaster (total: 257)
    • For animals of agronomic and veterinary relevance (see also ray-finned fish below):
      • 1384 added, 782 removed for Bos taurus (total: 1 985)
      • 590 added for Meleagris gallopavo (new species)
      • 432 added for Ovis aries (new species)
      • 79 added, 7 removed for Sus scrofa (total: 527)
      • 64 added for Capra hircus (new species)
      • 36 added for Gallus gallus (total: 84)
      • 3 added for Equus caballus (total: 248)
      • 1 added for Cavia porcellus (total: 284)
      • 1 added for Canis lupus familiaris (total: 162)
    • For non-model primates:
      • 813 added for Papio anubis (new species)
      • 409 added for Chlorocebus sabaeus (new species)
      • 37 added for Macaca fascicularis (new species)
      • 19 added for Macaca nemestrina (new species)
      • 18 added for Cercocebus atys (new species)
      • 18 added for Microcebus murinus (new species)
      • 14 added for Callithrix jacchus (new species)
      • 4 added for Macaca mulatta (total: 264)
    • For non-model ray-finned fish:
      • 333 added for Oryzias latipes (new species)
      • 274 added for Gasterosteus aculeatus (new species)
      • 165 added for Nothobranchius furzeri (new species)
      • 64 added for Astyanax mexicanus (new species)
      • 57 added for Gadus morhua (new species)
      • 45 added for Poecilia reticulata (new species)
      • 38 added for Astatotilapia calliptera (new species)
      • 36 added for Anguilla anguilla (new species)
      • 36 added for Scophthalmus maximus (new species)
      • 32 added for Neolamprologus brichardi (new species)
      • 32 added for Salmo salar (new species)
      • 24 added for Esox lucius (new species)
      • 21 added for Lepisosteus oculatus (new species)
    • Other species:
      • 274 added for Heterocephalus glaber (new species)
      • 57 added for Xenopus laevis (new species)
      • 52 added for Branchiostoma lanceolatum (new species)
      • 14 added for Latimeria chalumnae (new species)
      • 11 added for Manis javanica (new species)

  • The following species have been discontinued: Erinaceus europaeus, Drosophila ananassae, Drosophila mojavensis, Drosophila virilis, Drosophila yakuba.

  • We have updated all data from Model Organism Databases (BDGP, FlyBase, MGI, WormBase, Xenbase, ZFIN)

  • We have updated all genome information and all underlying ontologies used (e.g., Uberon)

You can still access Bgee version 14.2 at https://archives.bgee.org/14-2/.

2021-02-22

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.

2020-08-20

  • 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 the 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.

2020-03-26

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://archives.bgee.org/14-0/.

2019-10-05

2019-05-21

2019-05-12

  • 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 synonyms, and cross-references to other resources

2019-04-05

2018-02-14

Release of Bgee version 14.0

  • Release of the production version of Bgee release 14:

You can still access Bgee 13 at https://archives.bgee.org/13-2.

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 call;
    • "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 choose files to retrieve; inclusion of gene ranks (as used in gene pages) in call files.

You can still access Bgee 13 at https://archives.bgee.org/13-2/.

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 our new exclusive tool for gene expression enrichment analyses: TopAnat. This is a tool with absolutely no equivalent, developed 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 call 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 overview

2015-03-03

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

2014-12-19

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

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again