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

Abstract

ABSTRACTGEGA 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, GEGA’s 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