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bioRxiv · 10.1101/2024.03.13.584813

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

DEGALEZ, F.·Bardou, P.·Lagarrigue, S.
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Abstract

GEGA is a user-friendly tool to navigate through different genomics and functional information related to an enriched gene atlas in chicken that unifies the gene catalogues from the two reference databases, NCBI-RefSeq & EMBL-Ensembl/GENCODE, and four other additional rich resources as FAANG and NONCODE. Using the latest GRCg7b genome assembly, GEGA offers a total of 78,323 genes, including 24,102 protein-coding genes (PCGs) and 44,428 long non-coding RNAs (lncRNAs), greatly enhancing the number of genes provided by each resource separately. But GEGA is more than just a gene database. It offers a range of features that allow to go deeper into the functional aspects of these genes, e.g., by exploring their expression and co-expression profiles across 47 tissues from 36 datasets and 1400 samples, by discovering tissue-specific variations and their expression as a function of sex or age, by extracting their orthologous genes or their configuration related to the genomics closest gene. For the communities interested in one specific gene, a list of genes or a QTL region in chicken, GEGAs user-friendly interface enables efficient gene analysis, easy downloading of results and a multitude of graphical representations, from genomic information to detailed visualization of expression levels. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/584813v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@80db5org.highwire.dtl.DTLVardef@bc0f1forg.highwire.dtl.DTLVardef@84dd6corg.highwire.dtl.DTLVardef@e51c4b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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DEGALEZ, F., Bardou, P., Lagarrigue, S.. 2024-03-14. GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations. https://doi.org/10.1101/2024.03.13.584813

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