EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)
EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)
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EuRBPDB：用于真核 RNA 结合蛋白 (RBP) 注释、功能和肿瘤学研究的综合资源。
DOI：
10.1093/nar/gkz823
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Yin, Dong
中科院分区：
文献类型：
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作者：
Liao, Jian-You;Yang, Bing;Yin, Dong
RNA结合蛋白(RNAbindingProteins，RBPs)是一个大的蛋白质家族，通过与RNAs的相互作用，在几乎所有水平的基因调控中发挥重要作用，并参与许多生物学过程。然而，包括人类在内的真核限制性商业惯例的完整清单仍然无法获得。在此，我们基于rna结合域的计算分析和大规模的rna结合蛋白质组数据，系统地鉴定了162种真核生物中的限制性商业惯例，并建立了一个全面的真核生物限制性商业惯例数据库，http://EuRBPDB.syshospital.org).我们总共确定了311571个具有RBD的限制性商业惯例(对应于6368个直系同源基组)和3651个非规范的限制性商业惯例。EuRBPDB为每个RBP提供了详细的注释，包括基本信息和功能注释。此外，我们基于已发表的文献、PPI网络和大规模组学数据，在癌症生物学的背景下系统地研究了限制性商业惯例。为了便于探索限制性商业惯例的临床相关性，我们还设计了一个癌症网络界面，以系统和交互地展示限制性商业惯例在各种类型癌症中的生物学特征。EuRBPDB具有用户友好的Web界面，具有浏览和搜索功能，以及数据下载功能。我们期待EuRBPDB将成为RNA生物学和癌症生物学社区广泛使用的资源和平台。
RNA binding proteins (RBPs) are a large protein family that plays important roles at almost all levels of gene regulation through interacting with RNAs, and contributes to numerous biological processes. However, the complete list of eukaryotic RBPs including human is still unavailable. Here, we systematically identified RBPs in 162 eukaryotic species based on both computational analysis of RNA binding domains (RBDs) and large-scale RNA binding proteomic data, and established a comprehensive eukaryotic RBP database, EuRBPDB (http://EuRBPDB.syshospital.org). We identified a total of 311 571 RBPs with RBDs (corresponding to 6368 ortholog groups) and 3,651 non-canonical RBPs without known RBDs. EuRBPDB provides detailed annotations for each RBP, including basic information and functional annotation. Moreover, we systematically investigated RBPs in the context of cancer biology based on published literatures, PPI-network and large-scale omics data. To facilitate the exploration of the clinical relevance of RBPs, we additionally designed a cancer web interface to systematically and interactively display the biological features of RBPs in various types of cancers. EuRBPDB has a user-friendly web interface with browse and search functions, as well as data downloading function. We expect that EuRBPDB will be a widely-used resource and platform for both the communities of RNA biology and cancer biology.