Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks
Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks
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DOI：
10.1093/hmg/ddy239
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发表时间：
2018-10-01
影响因子：
3.5
通讯作者：
McGaughey, David M.
中科院分区：
文献类型：
--
作者：
Bryan, John M.;Fufa, Temesgen D.;McGaughey, David M.
人眼是由几个专门的组织组成的，这些组织引导，捕获和预处理信息以提供视觉。不同眼组织的基因表达已经在许多研究中用RNA-seq进行了广泛的分析。大型联盟项目也使用RNA-seq来研究除眼睛以外的许多不同人体组织的基因表达模式。与其他人体组织相比，还没有对来自多个眼组织的表达模式进行综合研究。我们整理了所有公开可用的健康人眼RNA-seq数据集以及数十种其他组织。我们使用这个完全集成的数据集来探测角膜，视网膜，视网膜色素上皮（RPE）-脉络膜复合体和其他人类组织之间的生物学过程和泛表达关系，并使用差异表达，聚类和基因本体论术语富集工具。我们还利用我们大量的视网膜和RPE脉络膜组织来构建第一个人类加权基因相关网络，并使用它们来突出已知的生物学途径和眼部基因疾病富集。我们还将公开可用的小鼠视网膜单细胞RNA-seq数据整合到我们的框架中进行验证和发现。最后，我们通过一个强大的交互式网络应用程序（https：//eyeintegration.nei.nih.gov/）提供所有这些数据、分析和可视化。
The human eye is built from several specialized tissues which direct, capture and pre-process information to provide vision. The gene expression of the different eye tissues has been extensively profiled with RNA-seq across numerous studies. Large consortium projects have also used RNA-seq to study gene expression patterning across many different human tissues, minus the eye. There has not been an integrated study of expression patterns from multiple eye tissues compared with other human body tissues. We have collated all publicly available healthy human eye RNA-seq datasets as well as dozens of other tissues. We use this fully integrated dataset to probe the biological processes and pan expression relationships between the cornea, retina, retinal pigment epithelium (RPE)-choroid complex, and the rest of the human tissues with differential expression, clustering and gene ontology term enrichment tools. We also leverage our large collection of retina and RPE choroid tissues to build the first human weighted gene correlation networks and use them to highlight known biological pathways and eye gene disease enrichment. We also have integrated publicly available single-cell RNA-seq data from mouse retina into our framework for validation and discovery. Finally, we make all these data, analyses and visualizations available via a powerful interactive web application (https://eyeintegration.nei.nih.gov/).