基于网络的基因表达分析——为解码健康和病变眼部组织铺平道路。
Web-based gene expression analysis-paving the way to decode healthy and diseased ocular tissue.
机构信息
Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital Muenster, Münster, Germany.
出版信息
Ophthalmologie. 2023 Jan;120(Suppl 1):59-65. doi: 10.1007/s00347-022-01721-4. Epub 2022 Sep 13.
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.
背景
使用 RNA 测序进行基因表达分析有助于提高对许多疾病的认识。数据库，如国家生物技术信息中心的基因表达综合数据库，提供了来自各种病变组织类型的 RNA 测序原始数据，但它们的分析需要先进的生物信息学技能。因此，特定的眼部数据库提供了不同眼部组织的转录谱，并且还能够进行直观的基于网络的数据分析。
目的
本叙述性综述的目的是概述眼部转录组数据库，并将其与在弗莱堡新建立的人类眼部转录组图谱进行比较。
方法
通过 PubMed 文献检索。
结果
共确定了 9 个专注于不同方面的眼部转录组数据库。iSyTE 和 Express 平台专门研究小鼠晶状体和视网膜发育过程中的基因表达，而 retina.tigem.it、Eye in a Disk 和 Spectacle 则专注于特定的眼部组织，如视网膜。Spectacle、UCSC Cell Browser 和 Single Cell Portal 允许直观地探索来自视网膜、脉络膜、角膜、虹膜、小梁网和巩膜标本的单细胞 RNA 测序数据。Ocular Tissue Database 包含各种健康眼部组织的微阵列图谱。Human Eye Transcriptome Atlas 提供了最大数量的不同眼部组织类型，包含了最多数量的眼部疾病，并具有通过方法学一致性实现的高水平质量。
结论
眼部转录组数据库提供了各种健康和病变眼部组织转录谱的全面和直观的见解。因此，它们有助于我们了解潜在的分子介质，支持假说的产生，并有助于寻找各种眼部疾病的新诊断和治疗靶点。
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