RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.
Nucleic Acids Res
; 46(D1): D327-D334, 2018 01 04.
Article
em En
| MEDLINE
| ID: mdl-29040692
ABSTRACT
More than 100 distinct chemical modifications to RNA have been characterized so far. However, the prevalence, mechanisms and functions of various RNA modifications remain largely unknown. To provide transcriptome-wide landscapes of RNA modifications, we developed the RMBase v2.0 (http//rna.sysu.edu.cn/rmbase/), which is a comprehensive database that integrates epitranscriptome sequencing data for the exploration of post-transcriptional modifications of RNAs and their relationships with miRNA binding events, disease-related single-nucleotide polymorphisms (SNPs) and RNA-binding proteins (RBPs). RMBase v2.0 was expanded with â¼600 datasets and â¼1 397 000 modification sites from 47 studies among 13 species, which represents an approximately 10-fold expansion when compared with the previous release. It contains â¼1 373 000 N6-methyladenosines (m6A), â¼5400 N1-methyladenosines (m1A), â¼9600 pseudouridine (Ψ) modifications, â¼1000 5-methylcytosine (m5C) modifications, â¼5100 2'-O-methylations (2'-O-Me), and â¼2800 modifications of other modification types. Moreover, we built a new module called 'Motif' that provides the visualized logos and position weight matrices (PWMs) of the modification motifs. We also constructed a novel module termed 'modRBP' to study the relationships between RNA modifications and RBPs. Additionally, we developed a novel web-based tool named 'modMetagene' to plot the metagenes of RNA modification along a transcript model. This database will help researchers investigate the potential functions and mechanisms of RNA modifications.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Processamento Pós-Transcricional do RNA
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Análise de Sequência de RNA
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Perfilação da Expressão Gênica
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Bases de Dados Genéticas
Tipo de estudo:
Risk_factors_studies
Limite:
Animals
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Humans
Idioma:
En
Ano de publicação:
2018
Tipo de documento:
Article