The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
| Autor: | Julien Roux, Sara S. Fonseca Costa, Philippe Moret, Julien Wollbrett, Sébastien Moretti, Frederic B. Bastian, Anne Niknejad, Komal Sanjeev, Valentine Rech de Laval, Yohan Jarosz, Marc Robinson-Rechavi, Amina Echchiki, Mar Gonzales-Porta, Angelique Escoriza, Emilie Person, Balazs Laurenczy, Aurélie Comte, Marta Rosikiewicz, Gilles Parmentier, Walid H. Gharib, Mathieu Seppey, Tarcisio Mendes de Farias, Patrick Roelli |
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| Rok vydání: | 2020 |
| Předmět: |
AcademicSubjects/SCI00010
RNA-Seq Computational biology Biology Transcriptome Bioconductor User-Computer Interface 03 medical and health sciences 0302 clinical medicine Databases Genetic Gene expression Genetics Animals Database Issue Animal species Gene Data Curation 030304 developmental biology 0303 health sciences Molecular Sequence Annotation R package Multiple data Gene Expression Regulation Data Annotation 030217 neurology & neurosurgery |
| Zdroj: | Nucleic acids research, vol. 49, no. D1, pp. D831-D847 Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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