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Related Experiment Video

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

Vinay Swamy1, David McGaughey1

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

Investigative Ophthalmology & Visual Science
|July 26, 2019
PubMed
Summary
This summary is machine-generated.

We created a human eye transcriptome database (EiaD) and web app (eyeIntegration) for querying gene expression across 19 eye and 54 body tissues. This resource aids researchers in testing hypotheses about human gene and transcript expression.

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Area of Science:

  • Genomics
  • Ophthalmology
  • Bioinformatics

Background:

  • Understanding human eye gene expression is crucial for diagnosing and treating ocular diseases.
  • Existing transcriptome databases lack comprehensive coverage of diverse human eye tissues.
  • A unified, accessible resource is needed to facilitate research on eye-specific gene regulation.

Purpose of the Study:

  • To develop an accessible and reliable RNA sequencing (RNA-seq) transcriptome database of healthy human eye tissues.
  • To create a matching web application for querying gene expression in eye and body tissues.
  • To provide a unified pan-human eye and body transcriptome dataset for hypothesis testing.

Main Methods:

  • Downloaded 1375 RNA-seq samples from the Genotype-Tissue Expression (GTEx) project as a non-eye reference.
  • Queried public repositories for 916 healthy, non-perturbed human eye tissue RNA-seq samples.
  • Utilized a Snakemake-based pipeline for data processing, normalization, differential expression analysis, and GO term enrichment, outputting an SQLite database (EiaD).
  • Rewrote the eyeIntegration web application to display the EiaD dataset.

Main Results:

  • The Eye in a Disk (EiaD) dataset integrates 916 eye and 1375 GTEx samples.
  • The eyeIntegration v1.0 portal visualizes human eye transcriptomes across 19 eye and 54 body tissues.
  • Analysis revealed high similarity between fetal and organoid retina transcriptomes, with distinct differences in specific gene families.

Conclusions:

  • The eyeIntegration v1.0 web app and EiaD dataset offer a powerful tool for the eye research community.
  • Researchers can now quickly test hypotheses on human gene and transcript expression across a wide range of tissues.
  • This resource enhances the ability to study gene expression patterns relevant to ocular health and disease.