ArticleBioinformatics (Oxford, England)2015
MicroRNA modules prefer to bind weak and unconventional target sites.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- CircRAD18 promotes glioblastoma proliferation, migration and invasion via the miR‑1231/LUC7L2 axis.International journal of molecular medicine · 2026Article
- New characteristics of MiRNA and IsomiR interactions with mRNA.Scientific reports · 2025Article
- A computational modeling of pri-miRNA expression.PloS one · 2024Article
- MicroRNAs: Small but Key Players in Viral Infections and Immune Responses to Viral Pathogens.Biology · 2023Review
- A deep learning method for miRNA/isomiR target detection.Scientific reports · 2022Article
- A two-stream convolutional neural network for microRNA transcription start site feature integration and identification.Scientific reports · 2021Article
- Computational annotation of miRNA transcription start sites.Briefings in bioinformatics · 2021Review
- Position-wise binding preference is important for miRNA target site prediction.Bioinformatics (Oxford, England) · 2020Article
- Expression of activating transcription factor 5 (ATF5) is mediated by microRNA-520b-3p under diverse cellular stress in cancer cells.PloS one · 2020Article
- Discovering sequence and structure landscapes in RNA interaction motifs.Nucleic acids research · 2019Article
- CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.Bioinformatics (Oxford, England) · 2018Article
- Dynamic and Modularized MicroRNA Regulation and Its Implication in Human Cancers.Scientific reports · 2017Article
- TarPmiR: a new approach for microRNA target site prediction.Bioinformatics (Oxford, England) · 2016Article
- Global Plant Stress Signaling: Reactive Oxygen Species at the Cross-Road.Frontiers in plant science · 2016Review
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Authors and funding
3 authors.
Funding
Abstract
motivationMicroRNAs (miRNAs) play critical roles in gene regulation. Although it is well known that multiple miRNAs may work as miRNA modules to synergistically regulate common target mRNAs, the understanding of miRNA modules is still in its infancy.
resultsWe employed the recently generated high throughput experimental data to study miRNA modules. We predicted 181 miRNA modules and 306 potential miRNA modules. We observed that the target sites of these predicted modules were in general weaker compared with those not bound by miRNA modules. We also discovered that miRNAs in predicted modules preferred to bind unconventional target sites rather than canonical sites. Surprisingly, contrary to a previous study, we found that most adjacent miRNA target sites from the same miRNA modules were not within the range of 10-130 nucleotides. Interestingly, the distance of target sites bound by miRNAs in the same modules was shorter when miRNA modules bound unconventional instead of canonical sites. Our study shed new light on miRNA binding and miRNA target sites, which will likely advance our understanding of miRNA regulation. AVAILABILITY AND IMPLEMENTATION: The software miRModule can be freely downloaded at http://hulab.ucf.edu/research/projects/miRNA/miRModule. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu.
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