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Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue
BACKGROUND: Gene expression analysis using RNA sequencing has helped to improve the understanding of many diseases. Databases, such as the Gene Expression Omnibus database of the National Center for Biotechnology Information provide RNA sequencing raw data from various diseased tissue types but thei...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Springer Medizin
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9469811/ https://www.ncbi.nlm.nih.gov/pubmed/36098765 http://dx.doi.org/10.1007/s00347-022-01721-4 |
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author | Wolf, Julian Lapp, Thabo Reinhard, Thomas Agostini, Hansjürgen Schlunck, Günther Lange, Clemens |
author_facet | Wolf, Julian Lapp, Thabo Reinhard, Thomas Agostini, Hansjürgen Schlunck, Günther Lange, Clemens |
author_sort | Wolf, Julian |
collection | PubMed |
description | BACKGROUND: Gene expression analysis using RNA sequencing has helped to improve the understanding of many diseases. Databases, such as the Gene Expression Omnibus database of the National Center for Biotechnology Information provide RNA sequencing raw data from various diseased tissue types but their analysis requires advanced bioinformatics skills. Therefore, specific ocular databases provide the transcriptional profiles of different ocular tissues and in addition enable intuitive web-based data analysis. OBJECTIVE: The aim of this narrative review is to provide an overview of ocular transcriptome databases and to compare them with the Human Eye Transcriptome Atlas newly established in Freiburg. METHODS: PubMed literature search. RESULTS: A total of nine ocular transcriptome databases focusing on different aspects were identified. The iSyTE and Express platforms specialize in gene expression during lens and retinal development in mice, whereas retina.tigem.it, Eye in a Disk, and Spectacle focus on selected ocular tissues such as the retina. Spectacle, UCSC Cell Browser and Single Cell Portal allow intuitive exploration of single cell RNA sequencing data derived from retinal, choroid, cornea, iris, trabecular meshwork and sclera specimens. The microarray profiles of a variety of healthy ocular tissues are included in the Ocular Tissue Database. The Human Eye Transcriptome Atlas provides the largest collection of different ocular tissue types, contains the highest number of ocular diseases and is characterized by a high level of quality achieved by methodological consistency. CONCLUSION: Ocular transcriptome databases provide comprehensive and intuitive insights into the transcriptional profiles of a variety of healthy and diseased ocular tissues. Thus, they improve our understanding of the underlying molecular mediators, support hypothesis generation and help in the search for new diagnostic and therapeutic targets for various ocular diseases. |
format | Online Article Text |
id | pubmed-9469811 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Springer Medizin |
record_format | MEDLINE/PubMed |
spelling | pubmed-94698112022-09-14 Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue Wolf, Julian Lapp, Thabo Reinhard, Thomas Agostini, Hansjürgen Schlunck, Günther Lange, Clemens Ophthalmologie Leitthema BACKGROUND: Gene expression analysis using RNA sequencing has helped to improve the understanding of many diseases. Databases, such as the Gene Expression Omnibus database of the National Center for Biotechnology Information provide RNA sequencing raw data from various diseased tissue types but their analysis requires advanced bioinformatics skills. Therefore, specific ocular databases provide the transcriptional profiles of different ocular tissues and in addition enable intuitive web-based data analysis. OBJECTIVE: The aim of this narrative review is to provide an overview of ocular transcriptome databases and to compare them with the Human Eye Transcriptome Atlas newly established in Freiburg. METHODS: PubMed literature search. RESULTS: A total of nine ocular transcriptome databases focusing on different aspects were identified. The iSyTE and Express platforms specialize in gene expression during lens and retinal development in mice, whereas retina.tigem.it, Eye in a Disk, and Spectacle focus on selected ocular tissues such as the retina. Spectacle, UCSC Cell Browser and Single Cell Portal allow intuitive exploration of single cell RNA sequencing data derived from retinal, choroid, cornea, iris, trabecular meshwork and sclera specimens. The microarray profiles of a variety of healthy ocular tissues are included in the Ocular Tissue Database. The Human Eye Transcriptome Atlas provides the largest collection of different ocular tissue types, contains the highest number of ocular diseases and is characterized by a high level of quality achieved by methodological consistency. CONCLUSION: Ocular transcriptome databases provide comprehensive and intuitive insights into the transcriptional profiles of a variety of healthy and diseased ocular tissues. Thus, they improve our understanding of the underlying molecular mediators, support hypothesis generation and help in the search for new diagnostic and therapeutic targets for various ocular diseases. Springer Medizin 2022-09-13 2023 /pmc/articles/PMC9469811/ /pubmed/36098765 http://dx.doi.org/10.1007/s00347-022-01721-4 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Leitthema Wolf, Julian Lapp, Thabo Reinhard, Thomas Agostini, Hansjürgen Schlunck, Günther Lange, Clemens Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
title | Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
title_full | Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
title_fullStr | Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
title_full_unstemmed | Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
title_short | Web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
title_sort | web-based gene expression analysis—paving the way to decode healthy and diseased ocular tissue |
topic | Leitthema |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9469811/ https://www.ncbi.nlm.nih.gov/pubmed/36098765 http://dx.doi.org/10.1007/s00347-022-01721-4 |
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