ArticleNucleic acids research2021
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Review
- Vape-Associated lncRNA Transcript 1 (VALT1) Amplifies the Tumorigenic Effects of e-Cigarette Vapor in Lung Epithelial Cells.Non-coding RNA · 2026Article
- Advancing Extracellular Vesicle Research: A Review of Systems Biology and Multiomics Perspectives.Proteomics · 2026Review
- GlycoRNAdb: a database of glycoRNA sequences, structures, abundance, and glycan information across tissues and cell lines.Nucleic acids research · 2026Article
- CircTarget: a comprehensive database of circRNA-target RNA interactions across multiple cell types.Nucleic acids research · 2026Article
- Targeting the HIF1A-UCA1-PTBP3 axis: a potential therapeutic strategy for head and neck cancer.BMC cancer · 2025Article
- Exploring the Potential of tsRNA as Biomarkers for Diagnosis and Treatment of Neurogenetic Disorders.Molecular neurobiology · 2025Review
- The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia.Cancer cell international · 2025Review
- Review
- Exosome miR-199a-5p modulated vascular remodeling and inflammatory infiltration of Takayasu's arteritis.Arthritis research & therapy · 2025Article
- Circular RNAs modulate cancer drug resistance: advances and challenges.Cancer drug resistance (Alhambra, Calif.) · 2025Article
- Sex-specific circRNA-miRNA-mRNA networks in peripheral blood mononuclear cells of patients with idiopathic pulmonary arterial hypertension: a pilot study.Frontiers in genetics · 2025Article
- Online Databases in Circular RNAs.Advances in experimental medicine and biology · 2025Review
- Small Nucleolar RNAs in Head and Neck Squamous Cell Carcinomas.Journal of dental research · 2025Review
- Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.ACS pharmacology & translational science · 2024Review
- Review
- International Society for Extracellular Vesicles Workshop. QuantitatEVs: multiscale analyses, from bulk to single extracellular vesicle.Journal of extracellular biology · 2024Article
- C2CDB: an advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs.Bioinformatics advances · 2024Article
- Unlocking the potential of non-coding RNAs in cancer research and therapy.Translational oncology · 2023Article
- Long non‑coding RNAs in multiple myeloma (Review).International journal of oncology · 2023Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs.
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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.