Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main 60590, Germany.
German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main 60590, Germany.
Sci Rep. 2016 Sep 1;6:32475. doi: 10.1038/srep32475.
Increasing evidence indicates the presence of long noncoding RNAs (lncRNAs) is specific to various cell types. Although lncRNAs are speculated to be more numerous than protein-coding genes, the annotations of lncRNAs remain primitive due to the lack of well-structured schemes for their identification and description. Here, we introduce a new knowledge database "ANGIOGENES" (http://angiogenes.uni-frankfurt.de) to allow for in silico screening of protein-coding genes and lncRNAs expressed in various types of endothelial cells, which are present in all tissues. Using the latest annotations of protein-coding genes and lncRNAs, publicly-available RNA-seq data was analyzed to identify transcripts that are expressed in endothelial cells of human, mouse and zebrafish. The analyzed data were incorporated into ANGIOGENES to provide a one-stop-shop for transcriptomics data to facilitate further biological validation. ANGIOGENES is an intuitive and easy-to-use database to allow in silico screening of expressed, enriched and/or specific endothelial transcripts under various conditions. We anticipate that ANGIOGENES serves as a starting point for functional studies to elucidate the roles of protein-coding genes and lncRNAs in angiogenesis.
越来越多的证据表明，长非编码 RNA（lncRNA）在各种细胞类型中存在特异性。尽管推测 lncRNA 的数量比蛋白质编码基因更多，但由于缺乏用于识别和描述它们的良好结构方案，lncRNA 的注释仍然很原始。在这里，我们介绍了一个新的知识库“ANGIOGENES”（http://angiogenes.uni-frankfurt.de），允许在各种类型的内皮细胞中表达的蛋白质编码基因和 lncRNA 的计算机筛选，这些细胞存在于所有组织中。使用最新的蛋白质编码基因和 lncRNA 注释，对公开可用的 RNA-seq 数据进行了分析，以鉴定在人类、小鼠和斑马鱼内皮细胞中表达的转录本。分析后的数据被整合到 ANGIOGENES 中，为转录组学数据提供一站式服务，以促进进一步的生物学验证。ANGIOGENES 是一个直观易用的数据库，允许在各种条件下对表达、富集和/或特定的内皮细胞转录本进行计算机筛选。我们预计 ANGIOGENES 将作为功能研究的起点，以阐明蛋白质编码基因和 lncRNA 在血管生成中的作用。
