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。大多数人类表达的基因仅通过表达序列标签（EST）已知。然而，许多眼组织中的cDNA文库，迄今已有助于dbEST的代表性很差。为了解决这种情况，一个项目，NEIBank，已经启动，以提高EST的覆盖范围的人眼，并开发一个分子百科全书的眼睛。已构建了几种人眼组织的cDNA文库，包括透镜、虹膜、RPE/脉络膜、视网膜和小梁网，并通过深度测序进行了检测。使用定制软件GRIST对来自每个未标准化文库的2，000至10，000个克隆进行测序、分析和聚类。透镜和虹膜库已经针对更深的序列进行了标准化。还创建了大鼠全眼、虹膜/睫状体/TM和视网膜以及小鼠全眼、视网膜和RPE/脉络膜的文库。其他图书馆，包括人类泪腺蛋白库也参与了分析。许多新的基因已被鉴定，包括opticin/oculoglycan（一种眼睛特异性富含亮氨酸的重复蛋白，其基因图谱接近ARMD），（与谷氨酰胺合成酶相关的丰富的透镜特异性转录物和透镜中终末分化的标记物，虹膜和RPE中的眼跨度蛋白，IEGF（虹膜表达的生长因子），其是VEGF/PDGF的相对物，和视网膜结合蛋白，一种与黄嘌呤结合蛋白相关的视网膜新分泌蛋白。此外，我们已经确定了许多重要的眼睛转录本的选择性剪接形式，可以产生修饰蛋白。这些包括较大版本的透镜膜蛋白MP 19/Lim 2和修饰版本的Nrl（视网膜转录因子）和Bestrophin（视网膜色素上皮的蛋白质）。总共约有20，000个眼部cDNA克隆，代表超过12，000个单独的GRIST簇（潜在基因），已被测序并组织在基于网络的数据库（neibank.nei.nih.gov）中，该数据库包含关键字和染色体位置数据。这项工作产生的DNA资源现在被用于创建用于眼部研究的微阵列。全球资源信息系统程序也用于分析防治荒漠化研究所项目的类似数据。

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.