ArticleBioinformatics (Oxford, England)2023
RNAenrich: a web server for non-coding RNA enrichment.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A Comparative Analysis of the Methylation Status of Non-Coding RNA Promoters in Fibroid and Matched Myometrium.International journal of molecular sciences · 2026Article
- Integrative transcriptomic analysis identifies shared coding and non-coding biomarkers in tongue squamous cell carcinoma across diverse populations.Discover oncology · 2026Article
- In vivo inhibition of TDO2 in fibroids results in widespread alteration in the tumor transcriptome.Clinical science (London, England : 1979) · 2026Article
- Transcriptomic and functional analysis of fibroid extracellular vesicles.Clinical science (London, England : 1979) · 2026Article
- Article
- A practical guide to functional enrichment analysis.Frontiers in bioinformatics · 2026Article
- E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins.RNA biology · 2025Article
- Exosomal small non-coding RNA profiling and the role of PIWI-interacting RNA pathway genes in Lumpy skin disease virus-infected bovines.Animal bioscience · 2025Article
- Article
- Differential Expression of Small Non-Coding RNAs in Uterine Leiomyomas.International journal of molecular sciences · 2025Article
- TetraRNA, a tetra-class machine learning model for deciphering the coding potential derivation of RNA world.Computational and structural biotechnology journal · 2025Article
- CytoLNCpred-a computational method for predicting cytoplasm associated long non-coding RNAs in 15 cell-lines.Frontiers in bioinformatics · 2025Article
- Modelling cell type-specific lncRNA regulatory network in autism with Cycle.BMC bioinformatics · 2024Article
- Localization is the key to action: regulatory peculiarities of lncRNAs.Frontiers in genetics · 2024Review
- Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.RNA biology · 2024Article
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13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationWith the rapid advances of RNA sequencing and microarray technologies in non-coding RNA (ncRNA) research, functional tools that perform enrichment analysis for ncRNAs are needed. On the one hand, because of the rapidly growing interest in circRNAs, snoRNAs, and piRNAs, it is essential to develop tools for enrichment analysis for these newly emerged ncRNAs. On the other hand, due to the key role of ncRNAs' interacting target in the determination of their function, the interactions between ncRNA and its corresponding target should be fully considered in functional enrichment. Based on the ncRNA-mRNA/protein-function strategy, some tools have been developed to functionally analyze a single type of ncRNA (the majority focuses on miRNA); in addition, some tools adopt predicted target data and lead to only low-confidence results.
resultsHerein, an online tool named RNAenrich was developed to enable the comprehensive and accurate enrichment analysis of ncRNAs. It is unique in (i) realizing the enrichment analysis for various RNA types in humans and mice, such as miRNA, lncRNA, circRNA, snoRNA, piRNA, and mRNA; (ii) extending the analysis by introducing millions of experimentally validated data of RNA-target interactions as a built-in database; and (iii) providing a comprehensive interacting network among various ncRNAs and targets to facilitate the mechanistic study of ncRNA function. Importantly, RNAenrich led to a more comprehensive and accurate enrichment analysis in a COVID-19-related miRNA case, which was largely attributed to its coverage of comprehensive ncRNA-target interactions. AVAILABILITY AND IMPLEMENTATION: RNAenrich is now freely accessible at https://idrblab.org/rnaenr/.
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