The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Frederic Bastian(SIB Swiss Institute of Bioinformatics), Julien Roux(SIB Swiss Institute of Bioinformatics), Anne Niknejad(SIB Swiss Institute of Bioinformatics), Aurélie Comte(SIB Swiss Institute of Bioinformatics), Sara Simões Costa(SIB Swiss Institute of Bioinformatics), Tarcisio Mendes de Farias(SIB Swiss Institute of Bioinformatics), Sébastien Moretti(SIB Swiss Institute of Bioinformatics), Gilles Parmentier(SIB Swiss Institute of Bioinformatics), Valentine Rech de Laval(SIB Swiss Institute of Bioinformatics), Marta Rosikiewicz(SIB Swiss Institute of Bioinformatics), Julien Wollbrett(SIB Swiss Institute of Bioinformatics), Amina Echchiki(SIB Swiss Institute of Bioinformatics), Angélique Escoriza(SIB Swiss Institute of Bioinformatics), Walid H. Gharib(SIB Swiss Institute of Bioinformatics), Mar Gonzales-Porta(SIB Swiss Institute of Bioinformatics), Yohan Jarosz(SIB Swiss Institute of Bioinformatics), Balazs Laurenczy(SIB Swiss Institute of Bioinformatics), Philippe Moret(SIB Swiss Institute of Bioinformatics), Emilie Person(SIB Swiss Institute of Bioinformatics), Patrick Roelli(SIB Swiss Institute of Bioinformatics), Komal Sanjeev(SIB Swiss Institute of Bioinformatics), Mathieu Seppey(SIB Swiss Institute of Bioinformatics), Marc Robinson‐Rechavi(SIB Swiss Institute of Bioinformatics)
Nucleic Acids Research
September 15, 2020
10.1093/nar/gkaa793
Cited by 201Open Access
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Abstract

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as 'healthy' or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.

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