ArticleNucleic acids research2016
An atlas of gene expression and gene co-regulation in the human retina.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data.BMC genomics · 2023Pooled it
- Retina-specific long non-coding RNAs associated with inherited retinal disease genes.Cellular and molecular life sciences : CMLS · 2026Article
- Systematic functional evaluation of CNGA1 missense variants associated with retinitis pigmentosa.Molecular medicine (Cambridge, Mass.) · 2026Article
- Paired DNA and RNA sequencing uncovers common and rare variation regulating human retinal gene expression.Nature communications · 2026Article
- RNA dysfunction in age-related macular degeneration: the role of U1 snRNP complex and neurodegenerative diseases.International journal of retina and vitreous · 2025Review
- Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling.eLife · 2025Article
- Experimental Framework for Assessing Mouse Retinal Regeneration Through Single-Cell RNA-Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Antisense Oligonucleotide STK-002 Increases OPA1 in Retina and Improves Mitochondrial Function in Autosomal Dominant Optic Atrophy Cells.Nucleic acid therapeutics · 2024Article
- A pipeline for identifying guide RNA sequences that promote RNA editing of nonsense mutations that cause inherited retinal diseases.Molecular therapy. Nucleic acids · 2024Article
- Retinoic acid signaling regulates spatiotemporal specification of human green and red cones.PLoS biology · 2024Article
- A proteogenomic atlas of the human neural retina.Frontiers in genetics · 2024Article
- Biallelic Variants in TULP1 Are Associated with Heterogeneous Phenotypes of Retinal Dystrophy.International journal of molecular sciences · 2023Article
- Expression and subcellular localization of USH1C/harmonin in human retina provides insights into pathomechanisms and therapy.Human molecular genetics · 2023Article
- Web-based gene expression analysis-paving the way to decode healthy and diseased ocular tissue.Die Ophthalmologie · 2023Review
- Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy.Journal of biomedical science · 2022Article
- Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy.American journal of human genetics · 2022Article
- Postnatal microcephaly and retinal involvement expand the phenotype of RPL10-related disorder.American journal of medical genetics. Part A · 2022Article
- Article
- Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitor cells.Scientific reports · 2021Article
- Multi-species single-cell transcriptomic analysis of ocular compartment regulons.Nature communications · 2021Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).
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