ArticleNucleic acids research2018
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 258 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
258 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Computational prediction of RNA modification site-disease associations: a systematic review.Briefings in bioinformatics · 2026Pooled it
- RNA methylation in vascular disease: a systematic review.Journal of cardiothoracic surgery · 2022Pooled it
- ALKBH10B mediated epitranscriptomic regulation enhances drought tolerance of Arabidopsis thaliana via hormonal cross-talk and sustained photosynthesis.Plant cell reports · 2026Article
- Enhancing tumor T cell antigen prediction by integrating deep protein representations.BMC bioinformatics · 2026Article
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- METTL3-dependent mJournal of translational medicine · 2026Article
- RNA modifications in cancer and their detection: a review.Japanese journal of clinical oncology · 2026Review
- Poxvirus infection triggers remodeling of host m⁶A epitranscriptome and benefits from the m⁶A regulatory responses.Virology journal · 2026Article
- DeepECC: a deep learning framework for genome-wide identification and analysis of human cancer eccDNAs.Nucleic acids research · 2026Article
- Domain-derived knowledge enabled machine learning and functional characterization of cancer-associated RNA methylation sites.BMC bioinformatics · 2026Article
- RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- VASN Enhances IGF2BP3 Stability via USP10 Deubiquitination to Promote Triple-negative Breast Cancer Paclitaxel Resistance.International journal of biological sciences · 2026Article
- THGC_MDA: a method for predicting the associations between mFrontiers in genetics · 2026Article
- Multi-omics characterization of RNA modification enzymes identifies NAT10 as a functionally validated prognostic biomarker in hepatocellular carcinoma.Frontiers in immunology · 2026Article
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- NSUN2 Negatively Regulates TP53 mRNA Stability to Promote the Malignant Progression of Nasopharyngeal Carcinoma.Cancers · 2025Article
- Article
- ATF3 Deficiency Exacerbates Ageing-Induced Atherosclerosis and Clinical Intervention Strategy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- CircPRKD3-loaded exosomes concomitantly elicit tumor growth inhibition and glioblastoma microenvironment remodeling via inhibiting STAT3 signaling.Neuro-oncology · 2025Article
- YModPred: an interpretable prediction method for multi-type RNA modification sites in S. cerevisiae based on deep learning.BMC biology · 2025Article
198 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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 ∼600 datasets and ∼1 397 000 modification sites from 47 studies among 13 species, which represents an approximately 10-fold expansion when compared with the previous release. It contains ∼1 373 000 N6-methyladenosines (m6A), ∼5400 N1-methyladenosines (m1A), ∼9600 pseudouridine (Ψ) modifications, ∼1000 5-methylcytosine (m5C) modifications, ∼5100 2'-O-methylations (2'-O-Me), and ∼2800 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.