ArticleNucleic acids research2020
PmiREN: a comprehensive encyclopedia of plant miRNAs.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
105 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea.Scientific reports · 2023Pooled it
- Heat stress-induced remodelling of lipid and microRNA networks in Brassica napus germinated pollen and pollen-derived small extracellular vesicles.Journal of experimental botany · 2026Article
- Genome-wide in-silico characterization and expression pattern analysis of GATA transcription factor family in carrot (Daucus carota subsp. sativus).Functional & integrative genomics · 2026Article
- Small RNA sequencing reveals drought-responsive microRNAs and regulatory networks in roots of mungbean genotypes differing in drought tolerance.BMC plant biology · 2026Article
- Synergistic regulation of abiotic stress adaptation by copper miRNAs miR398 and miR408 in melon.The Plant journal : for cell and molecular biology · 2026Article
- Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis.PLoS genetics · 2026Article
- Article
- Genome-Wide Identification of miRNAs and Pollen-Associated miRNA-Target Relationships inPlants (Basel, Switzerland) · 2026Article
- Rice and shine: a review of miRNA-mediated responses to abiotic stress inFrontiers in plant science · 2026Review
- Genome-wide bioinformatics analysis of the MATE gene family for abiotic stress tolerance in sunflower (Helianthus annuus L.).PloS one · 2026Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- A subclass of small RNAs is encoded by exons of protein-coding genes.BMC genomics · 2025Article
- Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network.International journal of molecular sciences · 2025Article
- Analysing the loss of embryogenic competence in long-term cell lines of Solanum betaceum Cav.: involvement of miR827, phosphate and sugar.BMC plant biology · 2025Article
- In silico identification and functional annotation of universal stress protein (USP) gene family in Chenopodium quinoa.Scientific reports · 2025Article
- WP-MOD: A multi-omics and taxonomy database for woody plants.Plant communications · 2025Article
- Identification and characterization of Eco-miR 169-EcNF-YA13 gene regulatory network reveal their role in conferring tolerance to dehydration and salinity stress in finger millet.Scientific reports · 2025Article
- Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis.Functional & integrative genomics · 2025Review
- Evolution of Plant Conserved microRNAs After Whole-Genome Duplications.Genome biology and evolution · 2025Article
- Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
45 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that function as diverse endogenous gene regulators at the post-transcriptional level. In the past two decades, as research effort on miRNA identification, function and evolution has soared, so has the demand for miRNA databases. However, the current plant miRNA databases suffer from several typical drawbacks, including a lack of entries for many important species, uneven annotation standards across different species, abundant questionable entries, and limited annotation. To address these issues, we developed a knowledge-based database called Plant miRNA Encyclopedia (PmiREN, http://www.pmiren.com/), which was based on uniform processing of sequenced small RNA libraries using miRDeep-P2, followed by manual curation using newly updated plant miRNA identification criteria, and comprehensive annotation. PmiREN currently contains 16,422 high confidence novel miRNA loci in 88 plant species and 3,966 retrieved from miRBase. For every miRNA entry, information on precursor sequence, precursor secondary structure, expression pattern, clusters and synteny in the genome, potential targets supported by Parallel Analysis of RNA Ends (PARE) sequencing, and references is attached whenever possible. PmiREN is hierarchically accessible and has eight built-in search engines. We believe PmiREN is useful for plant miRNA cataloguing and data mining, therefore a resource for data-driven miRNA research in plants.
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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.