RMBase

RMBase provides a transcriptome-wide database of RNA modifications by integrating epitranscriptome sequencing data to enable analysis of post-transcriptional modifications and their relationships with microRNA (miRNA) binding events, disease-related single-nucleotide polymorphisms (SNPs), and RNA-binding proteins (RBPs).

Key Features:

• Extensive Data Integration: Aggregates approximately 600 datasets comprising over 1.397 million modification sites from 47 studies across 13 species.
• Diverse RNA Modifications Cataloged: Contains information on more than 100 chemical modifications, including ~1.373 million N6-methyladenosines (m6A), ~5,400 N1-methyladenosines (m1A), ~9,600 pseudouridine (Ψ) sites, ~1,000 5-methylcytosines (m5C), ~5,100 2'-O-methylations (2'-O-Me), and ~2,800 other modification types.
• Innovative Modules: Provides a Motif Module with visualized sequence logos and position weight matrices (PWMs) for RNA modification motifs, a modRBP module to study interactions between RNA modifications and RBPs, and a modMetagene tool to plot metagene distributions of RNA modifications along transcript models.

Scientific Applications:

• Epitranscriptomics mapping: Enables transcriptome-wide identification and cataloging of RNA chemical modifications across multiple species and studies.
• miRNA–modification interplay analysis: Supports investigation of relationships between modification sites and microRNA (miRNA) binding events.
• SNP and disease association studies: Facilitates annotation and analysis of disease-related single-nucleotide polymorphisms (SNPs) in the context of RNA modifications.
• RBP interaction studies: Allows examination of interactions between RNA-binding proteins (RBPs) and RNA modifications using the modRBP module.
• Modification distribution visualization: Supports visualization of modification patterns across transcript models using metagene plotting (modMetagene).

Methodology:

Integrates epitranscriptome sequencing datasets, generates sequence logos and position weight matrices (PWMs) for modification motifs, and plots metagene distributions of RNA modifications along transcript models.