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RBP2GO:一个全面的跨物种 RNA 结合蛋白数据库,包含其相互作用和功能。

RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions.

机构信息

Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, 79106 Freiburg, Germany.

出版信息

Nucleic Acids Res. 2021 Jan 8;49(D1):D425-D436. doi: 10.1093/nar/gkaa1040.

Abstract

RNA-protein complexes have emerged as central players in numerous key cellular processes with significant relevance in health and disease. To further deepen our knowledge of RNA-binding proteins (RBPs), multiple proteome-wide strategies have been developed to identify RBPs in different species leading to a large number of studies contributing experimentally identified as well as predicted RBP candidate catalogs. However, the rapid evolution of the field led to an accumulation of isolated datasets, hampering the access and comparison of their valuable content. Moreover, tools to link RBPs to cellular pathways and functions were lacking. Here, to facilitate the efficient screening of the RBP resources, we provide RBP2GO (https://RBP2GO.DKFZ.de), a comprehensive database of all currently available proteome-wide datasets for RBPs across 13 species from 53 studies including 105 datasets identifying altogether 22 552 RBP candidates. These are combined with the information on RBP interaction partners and on the related biological processes, molecular functions and cellular compartments. RBP2GO offers a user-friendly web interface with an RBP scoring system and powerful advanced search tools allowing forward and reverse searches connecting functions and RBPs to stimulate new research directions.

摘要

RNA-蛋白质复合物已成为众多关键细胞过程中的核心参与者,它们在健康和疾病方面具有重要意义。为了进一步深入了解 RNA 结合蛋白 (RBP),已经开发了多种蛋白质组范围的策略来鉴定不同物种中的 RBP,从而产生了大量的实验鉴定和预测的 RBP 候选目录。然而,该领域的快速发展导致了孤立数据集的积累,阻碍了对其有价值内容的访问和比较。此外,缺乏将 RBP 与细胞途径和功能联系起来的工具。在这里,为了方便 RBP 资源的有效筛选,我们提供了 RBP2GO(https://RBP2GO.DKFZ.de),这是一个综合性数据库,包含了来自 53 项研究的 13 个物种的所有当前可用的蛋白质组范围数据集,这些数据集共鉴定了 22552 个 RBP 候选物。这些数据集与 RBP 相互作用伙伴以及相关的生物过程、分子功能和细胞区室的信息相结合。RBP2GO 提供了一个用户友好的 Web 界面,具有 RBP 评分系统和强大的高级搜索工具,允许进行正向和反向搜索,将功能和 RBP 联系起来,以激发新的研究方向。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0354/7778890/b3cbd3c87d53/gkaa1040gra1.jpg

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