neibank: Est Analysis And Bioinformatics For Ocular Geno

眼睛是一个复杂的系统，由各种发育起源的高度分化的组织组成。许多对眼睛功能至关重要的基因是组织特异性的，其中许多已知的基因与遗传性眼病有关。大多数人类表达基因只能通过表达序列标签（est）来了解。然而，迄今为止，许多眼部组织在促成dbEST的cDNA文库中表现不佳。为了解决这种情况，已经启动了一个项目，即NEIBank，以改进对人眼的无害环境技术的覆盖范围，并为人眼开发一个分子百科全书。构建了包括晶状体、虹膜、RPE/脉络膜、视网膜和小梁网在内的几种人眼组织的cDNA文库，并通过深度测序进行了检测。使用定制软件GRIST对每个非规范化库中的2000到10000个克隆进行了测序、分析和聚类。镜头和虹膜库已经标准化更深的序列。建立了大鼠全眼、虹膜/睫状体/TM和视网膜文库，小鼠全眼、视网膜和RPE/脉络膜文库。包括人类泪腺在内的其他文库也参与了分析。许多新的基因已经被发现，包括光学蛋白/眼聚糖（一种眼睛特异性的富含亮氨酸的重复蛋白，其基因定位接近ARMD），长蛋白（LGS）（一种丰富的晶状体特异性转录物，与谷氨酰胺合成酶相关，是晶状体终末分化的标记物），虹膜和RPE中的眼蛋白，IEGF（虹膜表达的生长因子），这是VEGF/PDGF的亲属，以及视网膜的一种新的分泌蛋白，与类黄酮结合蛋白相关。此外，我们已经确定了许多重要的眼睛转录本的可选剪接形式，这些剪接形式可能产生修饰蛋白。这些包括较大版本的晶状体膜蛋白MP19/Lim2和修改版本的Nrl，一种视网膜转录因子和Bestrophin，一种视网膜色素上皮蛋白。总共有大约20,000个眼部cDNA克隆，代表了超过12,000个单独的GRIST集群（潜在基因），已经在一个基于网络的数据库（neibank.nei.nih.gov）中进行了测序和组织，该数据库包含关键字和染色体定位数据。这项工作产生的DNA资源现在正被用于创建用于眼部研究的微阵列。GRIST程序也被用来分析非洲国家发展和疾病防治项目的类似数据。

The eye is a complex system of highly differentiated tissues of various developmental origins. Many genes essential for eye function are tissue-specific and many of those known are associated with genetic eye diseases. The majority of human expressed genes are known only through expressed sequence tags (ESTs). However many eye tissues have been poorly represented in the cDNA libraries that have so far contributed to dbEST. To address this situation a project, NEIBank, has been initiated to improve the EST coverage of the human eye and to develop a molecular encyclopedia for the eye. cDNA libraries for several human eye tissues, including lens,iris,RPE/choroid, retina and trabecular meshwork have been constructed and examined by in-depth sequencing. Between 2,000 and 10,000 clones from each un-normalized library have been sequenced, analyzed and clustered using custom software, GRIST. Lens and iris libraries have been normalized for deeper sequence. Libraries for rat whole eye, iris/ciliary body/TM and retina and mouse whole eye, retina and RPE/choroid have also been created. Other libraries, including human lacrimal galnd have been contributed to the analysis. Many novel genes have been identified, including opticin/oculoglycan (an eye-specific leucine-rich repeat protein whose gene maps close to ARMD), lengsin (LGS)(an abundant lens specific transcript related to glutamine synthetase and a marker for terminal differentiation in the lens, oculospanin in iris and RPE, IEGF (iris-expressed growth factor), which is a VEGF/PDGF relative, and retbindin, a novel secreted protein of the retina that is related to flavionoid binding proteins. In addition we have identifed numerous alternative splice forms of important eye transcripts that could give rise to modified proteins. These include a larger version of the lens membrane protein MP19/Lim2 and modifed versions of Nrl, a retina transcriptoin factor, and Bestrophin, a protein of the retinal pigment epithelium. In total, approximately 20,000 ocular cDNA clones, representing over 12,000 individual GRIST clusters (potential genes), have been sequenced and organized in a web-based database (neibank.nei.nih.gov)that contains keyword and chromosomal location data. The DNA resource generated by this work is now being used to create micro-arrays for ocular studies. The GRIST procedure is also being used to analyse similar data for projects in NIDCD.