EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2024-09-01 DOI:10.1016/j.jmb.2024.168571

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引用次数: 0

Abstract

Extracellular vesicles and particles (EVPs) play a crucial role in mediating cell-to-cell communication by transporting various molecular cargos, with small non-coding RNAs (ncRNAs) holding particular significance. A thorough investigation into the abundance and sorting mechanisms of ncRNA within EVPs is imperative for advancing their clinical applications. We have developed EVPsort, which not only provides an extensive overview of ncRNA profiling in 3,162 samples across various biofluids, cell lines, and disease contexts but also seamlessly integrates 19 external databases and tools. This integration encompasses information on associations between ncRNAs and RNA-binding proteins (RBPs), motifs, targets, pathways, diseases, and drugs. With its rich resources and powerful analysis tools, EVPsort extends its profiling capabilities to investigate ncRNA sorting, identify relevant RBPs and motifs, and assess functional implications. EVPsort stands as a pioneering database dedicated to comprehensively addressing both the abundance and sorting of ncRNA within EVPs. It is freely accessible at https://bioinfo.vanderbilt.edu/evpsort/.

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EVPsort：细胞外囊泡和颗粒中的小 ncRNA 图谱和分选图谱

细胞外囊泡和颗粒（EVPs）通过运输各种分子载体，在介导细胞间通讯方面发挥着至关重要的作用，其中小的非编码 RNA（ncRNA）尤为重要。深入研究 EVP 中 ncRNA 的丰度和分拣机制对于推动其临床应用至关重要。我们开发了 EVPsort，它不仅提供了 3162 份样本中各种生物流体、细胞系和疾病背景下 ncRNA 图谱的广泛概述，还无缝整合了 19 个外部数据库和工具。这种整合涵盖了 ncRNA 与 RNA 结合蛋白 (RBP)、主题、靶点、通路、疾病和药物之间的关联信息。凭借丰富的资源和强大的分析工具，EVPsort 扩展了其剖析功能，以研究 ncRNA 排序、识别相关 RBPs 和基调并评估功能影响。EVPsort 是一个开创性的数据库，致力于全面研究 EVPs 中 ncRNA 的丰度和排序。该数据库可通过以下网址免费访问：.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.