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

Overview

Journal NAR Genom Bioinform

Publisher Oxford University Press

Specialty Biology

Date 2024 Aug 19

PMID 39157583

Authors

Fabien Degalez

Philippe Bardou

Sandrine Lagarrigue

Affiliations

Soon will be listed here.

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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