iSyTE

To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed.为加速眼部发育及其相关缺陷的基因发现进程，我们此前开发了一款生物信息学资源工具iSyTE（integrated Systems Tool for Eye gene discovery）。然而，当前的iSyTE仅适用于晶状体组织，且主要基于转录组数据集构建。因此，为将iSyTE在蛋白质组层面拓展至其他眼部组织，我们对小鼠胚胎发育第14.5天（E14.5）的视网膜与视网膜色素上皮混合组织开展了高通量串联质谱（MS/MS）分析，每个样本平均鉴定出3300种蛋白质（样本量n=5）。基于高通量表达谱的基因发掘方法——无论采用转录组还是蛋白质组技术——均面临一项核心挑战：需从数千种已表达的RNA与蛋白质中筛选出优先研究的候选靶点。

搜集汇总

背景与挑战

背景概述

iSyTE是一个用于加速眼发育及相关缺陷基因发现的计算生物学工具，但现有版本仅针对晶状体组织且主要依赖转录组数据。为将其扩展到其他眼组织并提升至蛋白质组水平，本研究通过高通量质谱技术分析了小鼠胚胎视网膜与色素上皮复合组织，平均每个样本鉴定出约3300种蛋白质。