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Invest Ophthalmol Vis Sci. 2019 Jul 1;60(8):3236-3246. doi: 10.1167/iovs.19-27106.

Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

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1
Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States.

Abstract

Purpose:

We develop an accessible and reliable RNA sequencing (RNA-seq) transcriptome database of healthy human eye tissues and a matching reactive web application to query gene expression in eye and body tissues.

Methods:

We downloaded the raw sequence data for 1375 RNA-seq samples across 54 tissues in the Genotype-Tissue Expression (GTEx) project as a noneye reference set. We then queried several public repositories to find all healthy, nonperturbed, human eye-related tissue RNA-seq samples. The 916 eye and 1375 GTEx samples were sent into a Snakemake-based reproducible pipeline we wrote to quantify all known transcripts and genes, removes samples with poor sequence quality and mislabels, normalizes expression values across each tissue, perform 882 differential expression tests, calculate GO term enrichment, and output all as a single SQLite database file: the Eye in a Disk (EiaD) dataset. Furthermore, we rewrote the web application eyeIntegration (available in the public domain at https://eyeIntegration.nei.nih.gov) to display EiaD.

Results:

The new eyeIntegration portal provides quick visualization of human eye-related transcriptomes published to date by database version, gene/transcript, 19 eye tissues, and 54 body tissues. As a test of the value of this unified pan-eye dataset, we showed that fetal and organoid retina are highly similar at a pan-transcriptome level, but display distinct differences in certain pathways and gene families, such as protocadherin and HOXB family members.

Conclusions:

The eyeIntegration v1.0 web app serves the pan-human eye and body transcriptome dataset, EiaD. This offers the eye community a powerful and quick means to test hypotheses on human gene and transcript expression across 54 body and 19 eye tissues.

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