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

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_FD0CF4F734E7
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
Journal
Nucleic acids research
Author(s)
Bastian F.B., Roux J., Niknejad A., Comte A., Fonseca Costa S.S., de Farias T.M., Moretti S., Parmentier G., de Laval V.R., Rosikiewicz M., Wollbrett J., Echchiki A., Escoriza A., Gharib W.H., Gonzales-Porta M., Jarosz Y., Laurenczy B., Moret P., Person E., Roelli P., Sanjeev K., Seppey M., Robinson-Rechavi M.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
08/01/2021
Peer-reviewed
Oui
Volume
49
Number
D1
Pages
D831-D847
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
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.
Keywords
Genetics
Pubmed
Open Access
Yes
Funding(s)
Swiss National Science Foundation / 31003A_133011
Swiss National Science Foundation / 407540_167149
Swiss National Science Foundation / 31003A_153341
Swiss National Science Foundation / CRSII3_160723
Swiss National Science Foundation / 31003A_173048
Create date
31/05/2020 10:55
Last modification date
30/04/2021 7:16
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