RMBase

Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).

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RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data
PMID: 29040692

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:47.632694

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http://dx.doi.org/10.1093/nar/gkx934

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data PubMed citations: 117.

  117 articles citing: RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data

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  Nuclear Aurora kinase A switches m6A reader YTHDC1 to enhance an oncogenic RNA splicing of tumor suppressor RBM4. PMID:35361747

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  Identification of D Modification Sites Using a Random Forest Model Based on Nucleotide Chemical Properties. PMID:35328461

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  YTHDF1 upregulation mediates hypoxia-dependent breast cancer growth and metastasis through regulating PKM2 to affect glycolysis. PMID:35319018

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  CircRHBDD1 augments metabolic rewiring and restricts immunotherapy efficacy via m6A modification in hepatocellular carcinoma. PMID:35317519

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  Establishment and Validation of a 5 m6A RNA Methylation Regulatory Gene Prognostic Model in Low-Grade Glioma. PMID:35281815

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  29 m6A-RNA Methylation (Epitranscriptomic) Regulators Are Regulated in 41 Diseases including Atherosclerosis and Tumors Potentially via ROS Regulation - 102 Transcriptomic Dataset Analyses. PMID:35211628

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  MYC-activated RNA N6-methyladenosine reader IGF2BP3 promotes cell proliferation and metastasis in nasopharyngeal carcinoma. PMID:35136045

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  m6A modifications regulate intestinal immunity and rotavirus infection. PMID:35098923

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  Betacoronavirus-specific alternate splicing. PMID:35074468

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  RNA demethylase ALKBH5 in cancer: from mechanisms to therapeutic potential. PMID:35063010

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  Prediction and analysis of functional RNA structures within the integrative genomics viewer. PMID:35047817

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  Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences. PMID:35004647

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  ATXN2-mediated translation of TNFR1 promotes esophageal squamous cell carcinoma via m6A-dependent manner. PMID:34995801

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  m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. PMID:34986603

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  Low Expression of YTH Domain-Containing 1 Promotes Microglial M1 Polarization by Reducing the Stability of Sirtuin 1 mRNA. PMID:34975410

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  Analysis of N6-Methyladenosine Methylation Modification in Fructose-Induced Non-Alcoholic Fatty Liver Disease. PMID:34950107

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  The RNA-binding protein IMP2 drives a stromal-Th17 cell circuit in autoimmune neuroinflammation. PMID:34914635

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  YTHDC1-mediated VPS25 regulates cell cycle by targeting JAK-STAT signaling in human glioma cells. PMID:34863175

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  Methyltransferase-like 14 suppresses growth and metastasis of renal cell carcinoma by decreasing long noncoding RNA NEAT1. PMID:34813676

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  Epitranscriptomics of cardiovascular diseases (Review). PMID:34791505

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  Staem5: A novel computational approachfor accurate prediction of m5C site. PMID:34786208

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  The m6A "reader" YTHDF1 promotes osteogenesis of bone marrow mesenchymal stem cells through translational control of ZNF839. PMID:34772913

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  tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. PMID:34755848

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  Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. PMID:34747466

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  N 6-Methyladenosine Methylomic Landscape of Lung Tissues in Murine Acute Allergic Asthma. PMID:34737744

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  ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation. PMID:34723320

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  RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation. PMID:34718734

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  RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. PMID:34718726

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  Machine learning applications in RNA modification sites prediction. PMID:34712397

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  iTTCA-RF: a random forest predictor for tumor T cell antigens. PMID:34706730

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  The Latest Research Progress of m6A Modification and Its Writers, Erasers, Readers in Infertility: A Review. PMID:34568313

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  RNA m6A demethylase FTO-mediated epigenetic up-regulation of LINC00022 promotes tumorigenesis in esophageal squamous cell carcinoma. PMID:34544449

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  The role of RNA m5C modification in cancer metastasis. PMID:34512153

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  Degradation of WTAP blocks antiviral responses by reducing the m6 A levels of IRF3 and IFNAR1 mRNA. PMID:34467630

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  The functional roles, cross-talk and clinical implications of m6A modification and circRNA in hepatocellular carcinoma. PMID:34421350

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  Betacoronavirus-specific alternate splicing. PMID:34230929

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  The m6A reader IMP2 directs autoimmune inflammation through an IL-17- and TNFα-dependent C/EBP transcription factor axis. PMID:34215679

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  Genetic drivers of m6A methylation in human brain, lung, heart and muscle. PMID:34211177

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  Epigenetics: Roles and therapeutic implications of non-coding RNA modifications in human cancers. PMID:34188972

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  Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. PMID:34188054

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  RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA. PMID:34185947

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  LncRNAs and Available Databases. PMID:34160796

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  RNA modifications in hematopoietic malignancies: a new research frontier. PMID:34157073

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  Recent advances in functional annotation and prediction of the epitranscriptome. PMID:34136099

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  Methyl CpG binding protein 2 promotes colorectal cancer metastasis by regulating N6 -methyladenosine methylation through methyltransferase-like 14. PMID:34097350

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  Elucidating the Functions of Non-Coding RNAs from the Perspective of RNA Modifications. PMID:34065036

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  Enhanced antioxidant capacity prevents epitranscriptomic and cardiac alterations in adult offspring gestationally-exposed to ENM. PMID:33969789

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  Binding of RNA m6A by IGF2BP3 triggers chemoresistance of HCT8 cells via upregulation of ABCB1. PMID:33948366

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  M6ADD: a comprehensive database of m6A modifications in diseases. PMID:33906563

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  IGF2BP1, a Conserved Regulator of RNA Turnover in Cancer. PMID:33829040

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  Modeling multi-species RNA modification through multi-task curriculum learning. PMID:33744973

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  Accurate identification of RNA D modification using multiple features. PMID:33729104

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  Mining of RNA Methylation-Related Genes and Elucidation of Their Molecular Biology in Gallbladder Carcinoma. PMID:33718182

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  YTH Domain Proteins: A Family of m6A Readers in Cancer Progression. PMID:33692959

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  Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. PMID:33511416

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  IL-37 Confers Anti-Tumor Activity by Regulation of m6A Methylation. PMID:33489865

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  Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks. PMID:33274189

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  Systematic Investigation of mRNA N 6-Methyladenosine Machinery in Primary Prostate Cancer. PMID:33273988

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  Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma. PMID:33178585

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  m5CPred-SVM: a novel method for predicting m5C sites of RNA. PMID:33126851

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  The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma. PMID:33062408

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  RMVar: an updated database of functional variants involved in RNA modifications. PMID:33021671

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  m6A RNA Methylation in Cardiovascular Diseases. PMID:32910911

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  Oncogenic AURKA-enhanced N6-methyladenosine modification increases DROSHA mRNA stability to transactivate STC1 in breast cancer stem-like cells. PMID:32859993

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  m6A Reader: Epitranscriptome Target Prediction and Functional Characterization of N 6-Methyladenosine (m6A) Readers. PMID:32850851

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  m6A Reader YTHDC2 Promotes Radiotherapy Resistance of Nasopharyngeal Carcinoma via Activating IGF1R/AKT/S6 Signaling Axis. PMID:32850334

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  m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. PMID:32821938

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  MU-PseUDeep: A deep learning method for prediction of pseudouridine sites. PMID:32774783

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  Prediction of RNA Methylation Status From Gene Expression Data Using Classification and Regression Methods. PMID:32733123

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  Decoding the epitranscriptional landscape from native RNA sequences. PMID:32710622

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  The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer. PMID:32708015

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  Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. PMID:32670500

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  WITMSG: Large-scale Prediction of Human Intronic m6A RNA Methylation Sites from Sequence and Genomic Features. PMID:32655300

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  A Mini-review of the Computational Methods Used in Identifying RNA 5-Methylcytosine Sites. PMID:32655293

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  A Census and Categorization Method of Epitranscriptomic Marks. PMID:32630140

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  What do editors do? Understanding the physiological functions of A-to-I RNA editing by adenosine deaminase acting on RNAs. PMID:32603639

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  LITHOPHONE: Improving lncRNA Methylation Site Prediction Using an Ensemble Predictor. PMID:32582286

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  PSI-MOUSE: Predicting Mouse Pseudouridine Sites From Sequence and Genome-Derived Features. PMID:32565674

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  IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. PMID:32512182

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  BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472

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  Function and evolution of RNA N6-methyladenosine modification. PMID:32398960

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  The potential role of RNA N6-methyladenosine in Cancer progression. PMID:32398132

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  REPIC: a database for exploring the N6-methyladenosine methylome. PMID:32345346

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  Naturally occurring modified ribonucleosides. PMID:32301288

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  PIANO: A Web Server for Pseudouridine-Site (Ψ) Identification and Functional Annotation. PMID:32226440

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  Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators. PMID:32109416

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  m6Acorr: an online tool for the correction and comparison of m6A methylation profiles. PMID:31996134

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  Transcriptome-wide map of m6A circRNAs identified in a rat model of hypoxia mediated pulmonary hypertension. PMID:31931709

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  N6-Methyladenosine: A Novel RNA Imprint in Human Cancer. PMID:31921664

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  RNAInter in 2020: RNA interactome repository with increased coverage and annotation. PMID:31906603

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  Ontogenic mRNA expression of RNA modification writers, erasers, and readers in mouse liver. PMID:31891622

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  Epigenetic Regulation of m6A Modifications in Human Cancer. PMID:31887551

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  KIAA1429 contributes to liver cancer progression through N6-methyladenosine-dependent post-transcriptional modification of GATA3. PMID:31856849

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  The Prognostic Value of m6A RNA Methylation Regulators in Colon Adenocarcinoma. PMID:31823961

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  Investigating the energy crisis in Alzheimer disease using transcriptome study. PMID:31811163

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  The Biogenesis and Precise Control of RNA m6A Methylation. PMID:31810533

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  Predict Epitranscriptome Targets and Regulatory Functions of N 6-Methyladenosine (m6A) Writers and Erasers. PMID:31523126

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  XG-PseU: an eXtreme Gradient Boosting based method for identifying pseudouridine sites. PMID:31392406

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  m1A Regulated Genes Modulate PI3K/AKT/mTOR and ErbB Pathways in Gastrointestinal Cancer. PMID:31352195

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  Regulation of Viral Infection by the RNA Modification N6-Methyladenosine. PMID:31283446

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  RNAmod: an integrated system for the annotation of mRNA modifications. PMID:31147718

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  Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology. PMID:31047772

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  DNAmod: the DNA modification database. PMID:31016417

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  DRUM: Inference of Disease-Associated m6A RNA Methylation Sites From a Multi-Layer Heterogeneous Network. PMID:31001320

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  WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach. PMID:30993345

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  N6-Methyladenosine and Viral Infection. PMID:30891023

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  CVm6A: A Visualization and Exploration Database for m⁶As in Cell Lines. PMID:30781586

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  Identification of D Modification Sites by Integrating Heterogeneous Features in Saccharomyces cerevisiae. PMID:30678171

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  Gene2vec: gene subsequence embedding for prediction of mammalian N 6-methyladenosine sites from mRNA. PMID:30425123

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  POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819

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  The RNA Epitranscriptome of DNA Viruses. PMID:30185592

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  The Role of m6A/m-RNA Methylation in Stress Response Regulation. PMID:30048615

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  Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy. PMID:30013979

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  The m6A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5'-3' exoribonuclease XRN1. PMID:29970596

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  Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. PMID:29958477

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  Identifying RNA N6-Methyladenosine Sites in Escherichia coli Genome. PMID:29867860

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  Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. PMID:29859049
• http://dx.doi.org/10.1093/nar/gkx934

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More detailed information about this field from each metasource. ×

rna sequence databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

---

functional, regulatory and non-coding rna

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:47.632694

---

rna splicing

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:47.632694

---

gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:47.632694

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rna sequence functional, regulatory and non-coding rna rna splicing gene transcripts