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An atlas of gene expression and gene co-regulation in the human retina
- Source :
- Europe PubMed Central, Nucleic Acids Research, Nucleic acids research 44 (2016): 5773–5784. doi:10.1093/nar/gkw486, info:cnr-pdr/source/autori:Pinelli, Michele; Carissimo, Annamaria; Cutillo, Luisa; Cutillo, Luisa; Lai, Ching Hung; Mutarelli, Margherita; Moretti, Maria Nicoletta; Singh, Marwah Veer; Karali, Marianthi; Carrella, Diego; Pizzo, Mariateresa; Russo, Francesco; Ferrari, Stefano; Ponzin, Diego; Angelini, Claudia; Banfi, Sandro; Banfi, Sandro; Di Bernardo, Diego;/titolo:An atlas of gene expression and gene co-regulation in the human retina/doi:10.1093%2Fnar%2Fgkw486/rivista:Nucleic acids research/anno:2016/pagina_da:5773/pagina_a:5784/intervallo_pagine:5773–5784/volume:44
- Publication Year :
- 2016
-
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).
- Subjects :
- 0301 basic medicine
Gene isoform
Adult
Male
retina
gene co-regulation
Network, rna-seq, retina
Network
Biology
Genome
Transcriptome
Mitochondrial Proteins
03 medical and health sciences
Exon
Atlases as Topic
Gene expression
Genetics
Humans
Protein Isoforms
Gene Regulatory Networks
Eye Proteins
Gene
Aged
Genome, Human
Gene Expression Profiling
Alternative splicing
Web tools
pipeline
Chromosome Mapping
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Genomics
Exons
Middle Aged
Gene expression profiling
Alternative Splicing
030104 developmental biology
Gene Ontology
Gene Network
rna-seq
Female
Subjects
Details
- ISSN :
- 03051048
- Database :
- OpenAIRE
- Journal :
- Europe PubMed Central, Nucleic Acids Research, Nucleic acids research 44 (2016): 5773–5784. doi:10.1093/nar/gkw486, info:cnr-pdr/source/autori:Pinelli, Michele; Carissimo, Annamaria; Cutillo, Luisa; Cutillo, Luisa; Lai, Ching Hung; Mutarelli, Margherita; Moretti, Maria Nicoletta; Singh, Marwah Veer; Karali, Marianthi; Carrella, Diego; Pizzo, Mariateresa; Russo, Francesco; Ferrari, Stefano; Ponzin, Diego; Angelini, Claudia; Banfi, Sandro; Banfi, Sandro; Di Bernardo, Diego;/titolo:An atlas of gene expression and gene co-regulation in the human retina/doi:10.1093%2Fnar%2Fgkw486/rivista:Nucleic acids research/anno:2016/pagina_da:5773/pagina_a:5784/intervallo_pagine:5773–5784/volume:44
- Accession number :
- edsair.doi.dedup.....857d0dedc3378aeab910539ed881dc7f