Tool:Decode the Map of RNA Modifications from Epitranscriptome Sequencing Data
0
3
Entering edit mode
4.8 years ago
lsp03yjh ▴ 810

We have developed RMBase v2.0 to decode the map of RNA modifications (>100 different modification types) , as well as their relationships with microRNA binding events, disease-related SNPs or variations and RNA-binding proteins (RBP).

RMBase v2.0 was expanded with ~1402760 modification sites identified from 566 high-throughput epitranscriptome sequencing data (m1A-seq, Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq, Nm-seq) and public modification databases. It represented about 10 times expansion when compared to the previous release.

It contains ~1 379 400 N6-Methyladenosines (m6A), ~4 900 N1-Methyladenosines (m1A), ~9 600 pseudouridine (Ψ) modifications, ~1 000 5-methylcytosine (m5C) modifications, ~5 100 2′-O-methylations (2′-O-Me), and ~2 800 modifications of 100 other types.

We developed“Motif”module to provide both de novo identified position weight matrices (PWMs) and visualized logos of modification motifs.

We developed“modRBP” module to analyze the relationships of RNA modifications and RNA-binding Protein (RBP).

We developed a novel web-based tool named "modMetagene" for plotting metagenes of RNA modifications along a transcript model.

We developed modSNV and modSNP to decode the relationships between RNA modifications (m6A, m5C, 2′-O-Me) and variations (SNV, SNP), and link them to human cancers and other diseases.

RMBase v2.0 is freely available at http://rna.sysu.edu.cn/rmbase/.

RMBase v2.0 workflow

m6A m5C m1A pseudouridine SNP Tool • 2.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 2368 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6