GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
Journal Articles NAR Genomics and Bioinformatics Year : 2024

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations

Abstract

GEGA is a user-friendly tool designed to navigate through various genomic and functional information related to an enriched gene atlas in chicken that integrates the gene catalogues from the two reference databases, NCBI-RefSeq and EMBL-Ensembl/GENCODE, along with four additional rich resources such as FAANG and NONCODE. Using the latest GRCg7b genome assembly, GEGA encompasses a total of 78 323 genes, including 24 102 protein-coding genes (PCGs) and 44 428 long non-coding RNAs (lncRNAs), significantly increasing the number of genes provided by each resource independently. However, GEGA is more than just a gene database. It offers a range of features that allow us to go deeper into the functional aspects of these genes. Users can explore gene expression and co-expression profiles across 47 tissues from 36 datasets and 1400 samples, discover tissue-specific variations and their expression as a function of sex or age and extract orthologous genes or their genomic configuration relative to the closest gene. For the communities interested in a specific gene, a list of genes or a quantitative trait locus region in chicken, GEGA’s user-friendly interface facilitates efficient gene analysis, easy downloading of results and a multitude of graphical representations, from genomic information to detailed visualization of expression levels.
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hal-04685713 , version 1 (03-09-2024)

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Fabien Degalez, Philippe Bardou, Sandrine Lagarrigue. GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations. NAR Genomics and Bioinformatics, 2024, 6 (3), pp.lqae101. ⟨10.1093/nargab/lqae101⟩. ⟨hal-04685713⟩
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