Understanding the influence of gene expression on the molecular mechanisms underpinning human phenotypic diversity is fundamental to being able to predict health outcomes and treat disease. We have carried out whole transcriptome expression analysis on a series of eight normal human postmortem eyes by RNA sequencing. Here we present data showing that ∼80% of the transcriptome is expressed in the posterior layers of the eye and that there is significant differential expression not only between the layers of the posterior part of the eye but also between locations of a tissue layer. These differences in expression also extend to alternative splicing and splicing factors. Differentially expressed genes are enriched for genes associated with psychiatric, immune and cardiovascular disorders. Enrichment categories for gene ontology included ion transport, synaptic transmission and visual and sensory perception. Lastly, allele-specific expression was found to be significant forCFH,C3 andCFB, which are known risk genes for age-related macular degeneration. These expression differences should be useful in determining the underlying biology of associations with common diseases of the human retina, retinal pigment epithelium and choroid and in guiding the analysis of the genomic regions involved in the control of normal gene expression.
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Research Article|
August 01 2014
Comprehensive analysis of gene expression in human retina and supporting tissues
Publishing Partner:
Oxford University Press
Mingyao Li;
Mingyao Li
1
Department of Biostatistics and Epidemiology
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Cheng Jia;
Cheng Jia
1
Department of Biostatistics and Epidemiology
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Krista L. Kazmierkiewicz;
Krista L. Kazmierkiewicz
2
Department of Ophthalmology
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Anita S. Bowman;
Anita S. Bowman
2
Department of Ophthalmology
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Yichuan Liu;
Yichuan Liu
1
Department of Biostatistics and Epidemiology
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Neel A. Gupta;
Neel A. Gupta
8
College of Medicine
,Drexel University
,Philadelphia, PA
19104
,USA
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Harini V. Gudiseva;
Harini V. Gudiseva
2
Department of Ophthalmology
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Stephanie S. Yee;
Stephanie S. Yee
2
Department of Ophthalmology
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Tzvete Dentchev;
Tzvete Dentchev
3
Department of Dermatology
and
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James A. Kimble;
James A. Kimble
9
Retina Specialists of Alabama, Birmingham, AL
35294
,USA
10
Department of Ophthalmology
,University of Alabama School of Medicine
,Birmingham, AL
35294
,USA
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John S. Parker;
John S. Parker
10
Department of Ophthalmology
,University of Alabama School of Medicine
,Birmingham, AL
35294
,USA
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Jeffrey D. Messinger;
Jeffrey D. Messinger
10
Department of Ophthalmology
,University of Alabama School of Medicine
,Birmingham, AL
35294
,USA
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Hakon Hakonarson;
Hakon Hakonarson
4
Department of Pediatrics, The Perelman School of Medicine
,University of Pennsylvania
,Philadelphia
,PA
19104
,USA
6
Division of Pulmonary Medicine
and7
The Center for Applied Genomics
,The Children's Hospital of Philadelphia
,Philadelphia, PA
19104
,USA
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Christine A. Curcio;
Christine A. Curcio
10
Department of Ophthalmology
,University of Alabama School of Medicine
,Birmingham, AL
35294
,USA
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Dwight Stambolian
2
Department of Ophthalmology
*To whom correspondence should be addressed. Tel: +1 2158980305; Fax: +1 2155736728; Email:[email protected]
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Funders:
National Institutes of Health
,
Funder:
National Institutes of Health
Funder ID:
10.13039/100000002
Award/Grant ID:
NO AWARD
Arnold and Mabel Beckman Initiative for Macular Research
Funder:
Arnold and Mabel Beckman Initiative for Macular Research
Funder ID:
10.13039/100008226
Award/Grant ID:
NO AWARD
*To whom correspondence should be addressed. Tel: +1 2158980305; Fax: +1 2155736728; Email:[email protected]
†
The last two authors should be regarded as co-corresponding authors.
Publisher: Oxford University Press
Received:
November 12 2013
Revision Received:
January 21 2014
Accepted:
March 10 2014
Online ISSN: 1460-2083
Print ISSN: 0964-6906
Funders
Funder:
National Institutes of Health
Funder ID:
10.13039/100000002
Award/Grant ID:
NO AWARD
Funder:
Arnold and Mabel Beckman Initiative for Macular Research
Funder ID:
10.13039/100008226
Award/Grant ID:
NO AWARD
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected]
2014
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]
This work is licensed under a
Creative Commons Attribution-NonCommercial 4.0 International License
.
Publisher: Oxford University Press
Publication: Human Molecular Genetics
Hum Mol Genet (2014) 23 (15): 4001–4014.
Article history
Received:
November 12 2013
Revision Received:
January 21 2014
Accepted:
March 10 2014
Funders
Funder:
National Institutes of Health
Funder ID:
10.13039/100000002
Award/Grant ID:
NO AWARD
Funder:
Arnold and Mabel Beckman Initiative for Macular Research
Funder ID:
10.13039/100008226
Award/Grant ID:
NO AWARD