Open Access Datasets
GEGA - Download
Reference Files
| Name | Description | Size | |
|---|---|---|---|
| genomeAnnotation_GEGAv1_17022023_GRCg7b.dna.toplevel.fa | Genome Build (GRCg7b) used for alignment and quantification of gene expression. This file originates from Ensembl/Gencode (v107). The equivalent with the RefSeq nomenclature for chromosome naming can be found here. | 1.07 Go | |
|
genomeAnnotation_GEGAv1_17022023_GRCg7b_enriched6db_ NcbiEnsFragencodeDavisInraNoncode.gtf |
Genome annotation used for alignment and quantification of gene expression. As detailed in Degalez et al. 2024, gene models come from six sources gathered succesively: the “NCBI-RefSeq” (v106) and “EMBL-EBI Ensembl/GENCODE” (v107); the “FR-AgENCODE” and “FarmENCODE” FAANG pilot annotation projects, the gene annotation from Jehl et al. 2020, and, finally, the NONCODE annotation. | 1.4 Go | |
| genomeAnnotation_GEGAv1_17022023_GRCg7b_enriched6db_ NcbiEnsFragencodeDavisInraNoncode_ensembleGeneIdentifiers.gtf |
Alternative - Same genome annotation as shown for reference, but gene identifiers match those used by Ensembl to facilitate the use of specific tools or additional analyses. | 1.42 Go | |
| geneAnnotation_GEGAv1_17022023_GRCg7b_enriched6db_ NcbiEnsFragencodeDavisInraNoncode.tsv |
Gene annotation as available in the "Explore" tab. | 178.2 Mo | |
| geneAnnotationREADME_GEGAv1_17022023_GRCg7b_enriched6db_ NcbiEnsFragencodeDavisInraNoncode.xlsx |
README containing all the information concerning the various columns available in the .tsv file. This information is also available in the “Explore” tab via the “Show/Hide columns” hyperlink. | 32 Ko | |
| pcgHumanGTExOrthology_GEGAv1_17022023.txt | Protein-coding genes considered as orthologous between the chicken annotation used in GEGA and the GENCODE.v.26 human annotation used by the GTEx consortium. | 341 Ko |
Expression files - Global information
Expression files - Gene TPM
| Name | Description | Size | |
|---|---|---|---|
| gene_tpm_GEGAv1_17022023_gene_TPM.tsv | Gene TPMs. | 355.5 Mo | |
| gene_tpm_GEGAv1_17022023_gene_median_TPM.tsv | Median gene-level TPM by tissue. Median expression was calculated from the file "gene_tpm_GEGAv1_17022023_gene_TPM.tsv" | 16.7 Mo | |
| See on GTEx Website | Expression used for human genes are from the GTEx data available here. | NA |