ArticleInvestigative ophthalmology & visual science2019
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.
Article in Investigative ophthalmology & visual science, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 34 citations in OpenAlex.
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- Multilevel Genetic and Functional Assessment of an ARR3 Frameshift Variant in Early-Onset High Myopia.International journal of genomics · 2026Article
- HBS1L deficiency causes retinal dystrophy in a child and in a mouse model associated with defective development of photoreceptor cells.Disease models & mechanisms · 2024Article
- Platelet-activating factor receptor (PAFR) regulates neuronal maturation and synaptic transmission during postnatal retinal development.Frontiers in cellular neuroscience · 2024Article
- Genetic deficiency of ribosomal rescue factor HBS1L causes retinal dystrophy associated with Pelota and EDF1 depletion.bioRxiv : the preprint server for biology · 2023Article
- Contribution of common and rare variants to Asian neovascular age-related macular degeneration subtypes.Nature communications · 2023Article
- PLAE Web App Enables Powerful Searching and Multiple Visualizations Across One Million Unified Single-Cell Ocular Transcriptomes.Translational vision science & technology · 2023Article
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- Web-based gene expression analysis-paving the way to decode healthy and diseased ocular tissue.Die Ophthalmologie · 2023Review
- Transcriptional Profiling Provides New Insights into Organ Culture-Induced Changes in Human Donor Corneas.International journal of molecular sciences · 2022Article
- Gene Expression Data for Investigating Glaucoma Treatment Options and Pharmacology in the Anterior Segment, State-of-the-Art and Future Directions.Frontiers in neuroscience · 2022Review
- Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways.Frontiers in genetics · 2022Article
- Building the mega single-cell transcriptome ocular meta-atlas.GigaScience · 2021Article
- Myopia in African Americans Is Significantly Linked to Chromosome 7p15.2-14.2.Investigative ophthalmology & visual science · 2021Article
- A duplication on chromosome 16q12 affecting the IRXB gene cluster is associated with autosomal dominant cone dystrophy with early tritanopic color vision defect.Human molecular genetics · 2021Article
- North Carolina Macular Dystrophy: Phenotypic Variability and Computational Analysis of Disease-Associated Noncoding Variants.Investigative ophthalmology & visual science · 2021Article
- Let-7, Lin28 and Hmga2 Expression in Ciliary Epithelium and Retinal Progenitor Cells.Investigative ophthalmology & visual science · 2021Article
- Photoreceptor metabolic reprogramming: current understanding and therapeutic implications.Communications biology · 2021Review
- Haplotype-based genomic analysis reveals novel association ofJournal of biosciences · 2021Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.