{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T19:41:28Z","timestamp":1790710888641,"version":"4.1.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"S1","license":[{"start":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T00:00:00Z","timestamp":1663027200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T00:00:00Z","timestamp":1663027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Universit\u00e4tsklinikum Freiburg"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Ophthalmologie"],"published-print":{"date-parts":[[2023,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Gene expression analysis using RNA sequencing has helped to improve the understanding of many diseases. Databases, such as the <jats:italic>Gene Expression Omnibus database<\/jats:italic> of the <jats:italic>National Center for Biotechnology Information<\/jats:italic> 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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Objective<\/jats:title>\n                <jats:p>The aim of this narrative review is to provide an overview of ocular transcriptome databases and to compare them with the <jats:italic>Human Eye Transcriptome Atlas<\/jats:italic> newly established in Freiburg.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>PubMed literature search.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>A total of nine ocular transcriptome databases focusing on different aspects were identified. The <jats:italic>iSyTE<\/jats:italic> and <jats:italic>Express<\/jats:italic> platforms specialize in gene expression during lens and retinal development in mice, whereas <jats:italic>retina.tigem.it<\/jats:italic>, <jats:italic>Eye in a Disk<\/jats:italic>, and <jats:italic>Spectacle<\/jats:italic> focus on selected ocular tissues such as the retina. <jats:italic>Spectacle<\/jats:italic>, <jats:italic>UCSC Cell Browser<\/jats:italic> and <jats:italic>Single Cell Portal<\/jats:italic> 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\u00a0variety of healthy ocular tissues are included in the <jats:italic>Ocular Tissue Database<\/jats:italic>. The <jats:italic>Human Eye Transcriptome Atlas<\/jats:italic> provides the largest collection of different ocular tissue types, contains the highest number of ocular diseases and is characterized by a\u00a0high level of quality achieved by methodological consistency.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Ocular transcriptome databases provide comprehensive and intuitive insights into the transcriptional profiles of a\u00a0variety 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.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1007\/s00347-022-01721-4","type":"journal-article","created":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T15:11:57Z","timestamp":1663081917000},"page":"59-65","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Web-based gene expression analysis\u2014paving the way to decode healthy and diseased ocular tissue","Webbasierte Genexpressionsanalysen\u00a0\u2013 auf dem Weg zur molekularen Entschl\u00fcsselung gesunder und erkrankter Augengewebe. 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All authors are involved in the <i>Human Eye Transcriptome Atlas<\/i>, which was self-funded and published without commercial influence or interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"For this article no studies with human participants or animals were performed by any of the authors. All studies mentioned were in accordance with the ethical standards indicated in each case.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"The supplement containing this article is not sponsored by industry.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}