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 ourcurated 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 inSalmo salar (Atlantic salmon). We also now provide "physiological status", which holds information about the smoltification status of individuals, which is especially relevant forSalmo 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.

We are happy to announce that Bgee has been selected as aGlobal Core Biodata Resource by theGlobal 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 of52 GCBRs as of today.

Moreover, Bgee has been recognized as aRecommended Interoperability Resource byElixir. 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.

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 updatingDrosophila melanogaster data, with the integrationof the Fly Cell Atlas (FCA), and 3 other single-cell experiments. The methods established in this releasewill 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 comparablebetween other species and datasets:

• For instance, while the Fly Cell Atlas has been originally annotatedwith fly-specific vocabularies (i.e., FBbt ontology), Bgee reconnects these datato 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 theexpression calls for the fly geneeya ("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 signalto 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 theexperiment 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 containsthe data for one cell, see for instance thisSmart-Seq experiment in human.

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

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

• TheCurated 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.
• TheExpression calls page allows to browse and export all present/absent expression calls in Bgee, per species, gene, and condition.
• Both Curated 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 theGTEx experiment page

We have also added the following pages:

• The Scientific advisory board (SAB) of Bgee.
• Links to videos of courses or tutorials on Bgee.

Bgee is onMastodon

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, andbioinformatics tools
• Afternoon: 2 parallel hands-on sessions, each ½web ½RStats
  • Accessing curated transcriptome data
  • Bgee tools: making gene expression useful

Course information and registration

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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

Release of Bgee version 15.0

This is a major update of Bgee, with 28 new species; integration ofsingle-cell RNA-Seq full-length data; improved treatment of bulkRNA-Seq, and addition of new libraries; and improved statisticaltreatment to control for False Discovery Rate. Allin situhybridization data retrieved from Model Organism Databases, and allgenomes 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 thatBgee now includes single-cell RNA-Seq full-length data.We have designed statistical methods allowing to producereliable present expression calls and expression scores for thisdata type. We also use annotation procedures allowing to capturewith a high precision the cell types studied and their anatomicalorigin (post-composition of ontology terms). It isstraightforwardly integrated in all our tools, along with allother data (bulk RNA-Seq, Affymetrix, in situhybridization, Expressed Sequence Tags). For this release, we haveintegrated 1 481 libraries in human and mouse.

• 28 species have been added, while 5 species have beendiscontinued, 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 producepresent/absent expression calls. Rather than integrating booleancalls (where present calls always dominate), we produce a p-valuefor each expression call from each sample, and integrate these toproduce 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 generatelibraries (e.g., polyA, ribo-minus), and the gene types targeted(e.g., protein coding, miRNA). With this information, we produceabsent expression calls for a gene only if its type was accessibleto the RNA-Seq protocol used.

• Bgee 15.0 includes4 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 forHomo sapiens (total library count: 5 975)
    • 73 added, 13 removed forMus musculus (total: 566)
    • 14 added forDanio rerio (total: 161)
    • 4 added forDrosophila melanogaster (total: 257)
  • For animals of agronomic and veterinary relevance (see also ray-finned fish below):
    • 1384 added, 782 removed forBos taurus (total: 1 985)
    • 590 added forMeleagris gallopavo (new species)
    • 432 added forOvis aries (new species)
    • 79 added, 7 removed forSus scrofa (total: 527)
    • 64 added forCapra hircus (new species)
    • 36 added forGallus gallus (total: 84)
    • 3 added forEquus caballus (total: 248)
    • 1 added forCavia porcellus (total: 284)
    • 1 added forCanis lupus familiaris (total: 162)
  • For non-model primates:
    • 813 added forPapio anubis (new species)
    • 409 added forChlorocebus sabaeus (new species)
    • 37 added forMacaca fascicularis (new species)
    • 19 added forMacaca nemestrina (new species)
    • 18 added forCercocebus atys (new species)
    • 18 added forMicrocebus murinus (new species)
    • 14 added forCallithrix jacchus (new species)
    • 4 added forMacaca mulatta (total: 264)
  • For non-model ray-finned fish:
    • 333 added forOryzias latipes (new species)
    • 274 added forGasterosteus aculeatus (new species)
    • 165 added forNothobranchius furzeri (new species)
    • 64 added forAstyanax mexicanus (new species)
    • 57 added forGadus morhua (new species)
    • 45 added forPoecilia reticulata (new species)
    • 38 added forAstatotilapia calliptera (new species)
    • 36 added forAnguilla anguilla (new species)
    • 36 added forScophthalmus maximus (new species)
    • 32 added forNeolamprologus brichardi (new species)
    • 32 added forSalmo salar (new species)
    • 24 added forEsox lucius (new species)
    • 21 added forLepisosteus oculatus (new species)
  • Other species:
    • 274 added forHeterocephalus glaber (new species)
    • 57 added forXenopus laevis (new species)
    • 52 added forBranchiostoma lanceolatum (new species)
    • 14 added forLatimeria chalumnae (new species)
    • 11 added forManis 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 athttps://archives.bgee.org/14-2/.

Release of Bgee version 14.2

This is an incremental update of Bgee, improving data coveragemostly for animals of agronomic and veterinary relevance, and addingnew functionalities to the website

• On all gene pages you will now find links to ortholog and paraloggene pages, and links to directly run anexpression comparison analysis on them.
• We have madeTopAnat 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, andall the Bgee tools and download files, have been updatedaccordingly.

Other changes in this release:

• We have made changes to the way we propagate expression callsalong the graph of conditions: calls of absence of expression areno longer propagated to child anatomical entities, so that aninformation of absence of expression is more reliable from now on.
• We have also corrected some relations between anatomical entitiesthat were incorrectly missing in our database, improving thepropagation of expression calls as well.

• Update ofTopAnat
  • More information is now displayed about the list of genes you entered.
  • It is now possible to use data from any developmental and lifestage in the same analysis. Previously, it was only possible toperform 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 existingresults.
• Newpublication 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-Seqdataset, using the same genomes and ontologies as for the previousversion Bgee 14.0. New RNA-Seq libraries have been added; somelibraries previously integrated in Bgee have been discardedfollowing corrections and improvements of quality controls. TheAffymetrix,in situ hybridization, and EST datasets, are thesame as for the previous release of Bgee 14.0. All calls ofpresence/absence of expression, expression scores, and all the Bgeetools and download files, have been updated accordingly.

For most species in Bgee, notably non-human primates and farm anddomestic animals, this represents a major improvement of the anatomyand life stage coverage of the data, making all Bgee tools much moreuseful, notablyTopAnatand thegene pages.

• For human, 663 RNA-Seq libraries added, 13 removed, for a total of5,676 libraries in Bgee 14.1; there are now in total 1,794conditions annotated in Bgee, in 334 anatomical entities.

• For model organisms:

  • 197 libraries added for mouse (total 330 libraries); there arenow in total 13,821 conditions annotated in Bgee, in 3,275anatomical entities.
  • 193 added forXenopus tropicalis (total 259); 4,808conditions annotated in Bgee, in 395 anatomical entities.
  • 239 added forDrosophila melanogaster (total 253);5,704 conditions annotated in Bgee, in 1,138 anatomicalentities.
  • 80 added forDanio rerio (total 147); 7,307 conditionsannotated in Bgee, in 1,292 anatomical entities.
  • 9 libraries removed forCaenorhabditis elegans (total41), following improvements of quality controls; 745conditions annotated in Bgee, in 360 anatomical entities.

• Addition of data also in non-human primates:

  • 235 libraries added forPan troglodytes (total 250libraries); there are now in total 70 conditions annotated inBgee, in 26 anatomical entities.
  • 196 libraries added, 48 removed forMacaca mulatta(total 238); 50 conditions annotated in Bgee, in 25 anatomicalentities.
  • 1 library added forPan paniscus (total 13); 12conditions annotated in Bgee, in 7 anatomical entities.

• For farm and domestic animals:

  • 224 libraries added forEquus caballus (total 232);there are now in total 58 conditions annotated in Bgee, in 24anatomical entities.
  • 159 added forSus scrofa (total 169); 82 conditionsannotated in Bgee, in 41 anatomical entities.
  • 135 added forCanis lupus familiaris (total 141); 105conditions annotated in Bgee, in 54 anatomical entities.
  • 88 added forBos taurus (total 121); 22 conditions annotated in Bgee, in 19 anatomical entities.
  • 49 added forOryctolagus cuniculus (total 55); 24conditions annotated in Bgee, in 19 anatomical entities.
  • 3 added forGallus gallus (total 48); 30 conditionsannotated in Bgee, in 14 anatomical entities.
  • 23 added forFelis catus (total 32); 15 conditionsannotated in Bgee, in 11 anatomical entities.
  • 19 added forCavia porcellus (total 28); 6 conditionsannotated in Bgee, in 5 anatomical entities.

• Other species with changes:

  • 89 libraries added forMonodelphis domestica (total108); there are now in total 51 conditions annotated in Bgee,in 24 anatomical entities.
  • 70 added forRattus norvegicus (total 106); 64conditions annotated in Bgee, in 22 anatomical entities.
  • 27 added forAnolis carolinensis (total 31); 20conditions annotated in Bgee, in 15 anatomical entities.
  • 4 added forOrnithorhynchus anatinus (total 21); 16conditions annotated in Bgee, in 9 anatomical entities.
  • 2 added, 4 removed forDrosophila simulans (total 15);7 conditions annotated in Bgee, in 4 anatomical entities.
  • 4 removed forDrosophila pseudoobscura (total 10); 6conditions annotated in Bgee, in 4 anatomical entities.

• Update of theExpression Comparison page to display expression scores rather than expression ranks.

• Update of the menu, of thecollaboration page of theSPARQL documentation page(notably to access archived version of Bgee, starting with Bgee 14.0).

You can still access Bgee version 14.0 athttps://archives.bgee.org/14-0/.

• New score ongene pages.
• Newspecies page.
• Update of theexpression comparison
  • Better sorting approach.
  • Possibility to export results (copy to clipboard or TSV).
• Improve findability of data by addingBioschemas markup.

• Newexpression comparison page.
• Newanatomical homology page.
• New resource pages:R packages,Annotations,Ontologies andSource code pages.
• NewData dumps andSPARQL endpoint pages.
• NewBgee collaborations page.
• Update of the menu

• Update of thegene 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

• Newprivacy policy page
• NewFAQ page where we address common user queries
• Newdocumentation pagespecific to GTEx project to learn how we integrated these data into Bgee
• Update to Bgee 14.0 of thegene expression call documentation
• Update of thedata 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 athttps://archives.bgee.org/13-2.

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, removingunhealthy samples; seehuman data.

• Improved quality annotation of calls: replacement of "lowquality" / "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 toretrieve; inclusion of gene ranks (as used in gene pages) in callfiles.

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

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 rankingalgorithm allowing to discover the most relevant anatomicalentities and life stages where a gene is expressed. We hopethat you will appreciate the noticeable improvements.

  • The gene page has been updated to display the rank scores ofconditions where a gene is expressed, allowing to easilyidentify major functional shifts in gene expression.

• Give a try to this updated ranking by searching for your favoritegene, or by using the example links, on thegene search page.

• We now display more information about the sources of data used inBgee, see the newdata source page, and new information added to the gene pages.

Release of our newBgeeDB R package,a package for the annotation and gene expression data download fromBgee database into R, and TopAnat analysis (see alsoBioconductor website).

Various improvements of our new interface.

Release of our newgene page,allowing to discover the most relevant conditions where a gene isexpressed. This update also includes an important revamping of ourinterfaces.

Major update ofTopAnat.Happy Christmas!

We are happy to release our new exclusive tool for gene expressionenrichment analyses:TopAnat.This is a tool with absolutely no equivalent, developed incollaboration with the Web-Team of the SIB Swiss Institute ofBioinformatics. 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 mousein situ data from MGI, seemouse data.
• Differential expression data have been added forzebrafish,chimpanzee,gorilla,andopossum.
• Addition of new multi-species differential expression data, seefor instancechimpanzee/macaque comparison.
• New format to provide gene orthology information in multi-speciesfiles, see for instanceOMA Hierarchical orthologous groups documentation.
• Removal of data incorrectly considered as normal inC. elegans, seeworm data.
• Improved filtering of propagated no-expression calls. As a result,complete expression call files do not contain invalid conditionsanymore.
• Filtering of invalid developmental stages for differentialexpression analyses.

Release of the multi-species differential expression data (acrossanatomy) for 6 groups, seedownload overview

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

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