PDbase：一个使用黑质 EST 构建的帕金森病相关基因和遗传变异数据库。
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs.
机构信息
Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea.
出版信息
BMC Genomics. 2009 Dec 3;10 Suppl 3(Suppl 3):S32. doi: 10.1186/1471-2164-10-S3-S32.
BACKGROUND
Parkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have created PD-related research resources. However, resources for brain and PD studies are still lacking. Therefore, we have constructed a database of PD-related gene and genetic variations using the substantia nigra (SN) in PD and normal tissues. In addition, we integrated PD-related information from several resources.
RESULTS
We collected the 6,130 SN expressed sequenced tags (ESTs) from brain SN normal tissues and PD patients SN tissues using full-cDNA library and normalized cDNA library construction methods from our previous study. The SN ESTs were clustered in 2,951 unigene clusters and assigned in 2,678 genes. We then found up-regulated 57 genes and down-regulated 48 genes by comparing normal and PD SN ESTs frequencies with over 0.9 cut-off probability of differential expression based on the Audic and Claverie method. In addition, we integrated disease-related information from public resources. To examine the characteristics of these PD-related genes, we analyzed alternative splicing events, single nucleotide polymorphism (SNP) markers located in the gene regions, repeat elements, gene regulation elements, and pathways and protein-protein interaction networks.
CONCLUSION
We constructed the PDbase database to capture the PD-related gene, genetic variation, and functional elements. This database contains 2,698 PD-related genes through ESTs discovered from human normal and PD patients SN tissues, and through integrating several public resources. PDbase provides the mitochondrion proteins, microRNA gene regulation elements, single nucleotide polymorphisms (SNPs) markers within PD-related gene structures, repeat elements, and pathways and networks with protein-protein interaction information. The PDbase information can aid in understanding the causation of PD. It is available at http://bioportal.kobic.re.kr/PDbase/. Supplementary data is available at http://bioportal.kobic.re.kr/PDbase/suppl.jsp.
背景
帕金森病（PD）是最常见的神经退行性疾病之一，其临床特征为运动功能受损。由于 PD 的病因多样且复杂，许多研究人员已经创建了与 PD 相关的研究资源。然而，用于大脑和 PD 研究的资源仍然缺乏。因此，我们使用 PD 和正常组织中的黑质（SN）构建了 PD 相关基因和遗传变异数据库。此外，我们整合了来自多个资源的 PD 相关信息。
结果
我们从前一项研究中使用全 cDNA 文库和标准化 cDNA 文库构建方法，从脑 SN 正常组织和 PD 患者 SN 组织中收集了 6,130 个 SN 表达序列标签（EST）。SN EST 聚类为 2,951 个非重叠基因簇，并分配到 2,678 个基因中。然后，我们通过比较正常和 PD SN EST 频率，根据 Audic 和 Claverie 方法以超过 0.9 的差异表达概率阈值，找到了 57 个上调基因和 48 个下调基因。此外，我们整合了来自公共资源的疾病相关信息。为了检查这些 PD 相关基因的特征，我们分析了选择性剪接事件、位于基因区域的单核苷酸多态性（SNP）标记、重复元件、基因调控元件以及通路和蛋白质-蛋白质相互作用网络。
结论
我们构建了 PDbase 数据库以捕获 PD 相关基因、遗传变异和功能元件。该数据库通过从人类正常和 PD 患者 SN 组织中发现的 EST，以及通过整合几个公共资源，包含 2698 个 PD 相关基因。PDbase 提供了线粒体蛋白、microRNA 基因调控元件、PD 相关基因结构内的单核苷酸多态性（SNP）标记、重复元件以及通路和具有蛋白质-蛋白质相互作用信息的网络。PDbase 信息有助于理解 PD 的发病机制。它可在 http://bioportal.kobic.re.kr/PDbase/ 上获取。补充数据可在 http://bioportal.kobic.re.kr/PDbase/suppl.jsp 上获取。
Zotero 插件