RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications.
RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications.
复制标题
RMBase v3.0：解码RNA修饰的景观，机制和功能。
DOI：
10.1093/nar/gkad1070
复制
发表时间：
2024-01-05
影响因子：
14.9
通讯作者：
中科院分区：
文献类型：
--
作者：
虽然已经确定了170多种化学修饰，但它们的流行程度、机制和功能在很大程度上仍然未知。为了能够综合分析各种RNA修饰谱，我们开发了RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/)，这是一个由八个模块组成的综合平台。这些模块有助于探索转录组的景观，生物发生，相互作用和RNA修饰的功能。通过使用新颖的管道挖掘数千个表转录组数据集，“RNA修饰”模块揭示了62个物种的73个RNA修饰图谱。“基因”模块允许通过基因和转录本检索RNA修饰概况和集群。“机制”模块探索23382个酶催化或snorna引导的修饰位点，以阐明其生物发生机制。“共定位”模块系统地阐述了各种细胞系中14种组蛋白修饰和6种RNA修饰之间的潜在相关性。“RMP”模块研究了18种癌症中146种rna修饰蛋白（RMP）的差异表达谱。Interactome整合了73种RNA修饰与RBP结合事件、miRNA靶点和snp之间的相互作用关系。“Motif”阐明了从表转录组数据集中鉴定出的11种RNA修饰的富集基序。“工具”引入了一种新颖的基于网络的“modGeneTool”，用于注释修改。总之，RMBase v3.0为研究RNA修饰提供了各种资源和工具。
Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the ‘RNA Modifications’ module reveals the map of 73 RNA modifications of 62 species. the ‘Genes’ module allows to retrieve RNA modification profiles and clusters by gene and transcript. The ‘Mechanisms’ module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The ‘Co-localization’ module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The ‘RMP’ module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The ‘Interactome’ integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The ‘Motif’ illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The ‘Tools’ introduces a novel web-based ‘modGeneTool’ for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.
登录
查看更多内容
RNA 假尿苷化：对旧修饰的新见解。
影响因子：
13.8
作者：
Ge, Junhui;Yu, Yi-Tao
通讯作者：
Yu, Yi-Tao
影响因子：
14.9
作者：
Chan PP;Lowe TM
通讯作者：
Lowe TM
影响因子：
10.5
作者：
Ke S;Alemu EA;Mertens C;Gantman EC;Fak JJ;Mele A;Haripal B;Zucker-Scharff I;Moore MJ;Park CY;Vågbø CB;Kusśnierczyk A;Klungland A;Darnell JE Jr;Darnell RB
通讯作者：
Darnell RB
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P
影响因子：
14.9
作者：
Boccaletto P;Stefaniak F;Ray A;Cappannini A;Mukherjee S;Purta E;Kurkowska M;Shirvanizadeh N;Destefanis E;Groza P;Avşar G;Romitelli A;Pir P;Dassi E;Conticello SG;Aguilo F;Bujnicki JM
通讯作者：
Bujnicki JM