LNChickenAtlas · project overview

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Overview

We propose chicken gene atlases that are enriched in long non-coding RNA (lncRNAs) genes and a few protein-coding genes by gathering gene models from several genome annotations, including in particular EMBL-EBI Ensembl and NCBI RefSeq. The gene-enriched atlases are available for three genome assemblies: GalGal5, GRCg6a, and the most recent GRCg7b.

Each gene of these atlases is provided with "functional" and "genomic" information (see table below). "Functional" annotation includes various features like the official short gene Name, full gene name, human and mouse orthologous name (iD, HGNC name), expression profiles in various tissues (~40 for the last version associated to the GRCg7), tissue specificity score, etc. "Genomic" information provides the position of the genes and transcripts, the exon and intron numbers, the closest gene, the overlap with a miRNA gene, etc.

In addition, a vcf file is provided with a set of ~9.9M SNPs called from RNA-seq data.

Resulting annotations

Galgal5 - Ensembl v94 GRCg6a - Ensembl v101 GRCg7b - Ensembl v107 - NCBI RefSeq v106

Source	# protein-coding genes	# long non-coding genes	Genome annotation	Gene annotation °°
Ensembl*	18,346	4,643	ens94.gtf.gz	gnAnnotEns94.tsv.gz README.pdf
Gene-enriched atlas***	19,545	30,084	GeneRichEns94.gtf.gz	gnAnnotLNCextendedEns94.tsv.gz README.pdf

Source	# protein-coding genes	# long non-coding genes	Genome annotation	Gene annotation °°
Ensembl*	16,878	5,506	Ens101.gtf.gz	gnAnnotEns101.tsv.gz README.pdf
Gene-enriched atlas***	17,921	25,082	GeneRichEns101.gtf.gz	gnAnnotLNCextendedEns101.tsv.gz README.pdf

Source	# protein-coding genes	# long non-coding genes	Genome annotation	Gene annotation °°
Ensembl*	17,007	11,944	Ens107.gtf.gz	(in progress) (in progress)
NCBI RefSeq*	18,024	5,791	RefSeq106.gtf.gz	(in progress) (in progress)
Gene-enriched atlas**	23,926	44,428	GeneRichNCBI106Ens107.gtf.gz	(in progress) (in progress)

Variant file with ~9.9M SNPs called from RNA-seq data (Galgal5, compressed vcf): SNPlist_galgal5.vcf.gz

* reference annotation from Ensembl or NCBI RefSeq

** catalogue extending the Ensembl and RefSeq references by gathering Ensembl, RefSeq and other databases (FAANG databases from University of Davis and INRAE (FR-AgENCODE and NONCODE) (see Degalez et al, in preparation).

*** catalogue extending the Ensembl reference with LNC from 3 public databases (NCBI, NONCODE, ALDB) and other sources (see Jehl et al 2020).

°° a tab-separated text file (.tsv.gz, compressed) providing 3 types of information about each coding and non-coding gene (see below) and a pdf readme file describing these informations with some associated statistics.

genomic features like genomic location, orthology, FEELnc classifications (enriched by Jehl et al 2020),
expression patterns in different multi-tissue datasets,
ontologies as GO terms and MGI phenotypes.

References: If these annotations are used, please cite Jehl, Frédéric et al. "An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues." Scientific reports vol. 10,1 20457. 24 Nov. 2020. doi:10.1038/s41598-020-77586-x. If the SNPlist_galgal5.vcf.gz variant file is used, please cite Jehl, Frédéric et al. "RNA-seq data for reliable SNP detection and genotype calling: interest for coding variant characterization and cis-regulation analysis by allele-specific expression in livestock species." Frontiers Genet 2021 Jun 28;12:655707.doi: 10.3389/fgene.2021.655707

Contact: Mail to Sandrine Lagarrigue.