ArticleNature communications2018
microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- miR-29b as an Anti-Fibrotic Therapeutic: Mechanisms, Disease Biology and Translational Opportunities.Cells · 2026Review
- Differential expression of the lncRNA MIR17HG and miR-18a/miR-20a as candidate ncRNA signatures in stage II/III breast cancer and bioinformatic analysis of ncRNA-mRNA regulatory axes.Iranian journal of basic medical sciences · 2026Article
- Article
- microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites.Briefings in bioinformatics · 2024Article
- TRPM2-AS promotes ovarian cancer cell proliferation and inhibits cell apoptosis by upregulating the nearby gene TRPM2 via miR-6764-5p.Cell division · 2024Article
- Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.ACS pharmacology & translational science · 2024Review
- Functional microRNA-targeting drug discovery by graph-based deep learning.Patterns (New York, N.Y.) · 2024Article
- TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs.Nucleic acids research · 2024Article
- Article
- A novel necroptosis related gene signature and regulatory network for overall survival prediction in lung adenocarcinoma.Scientific reports · 2023Article
- DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts.Nucleic acids research · 2023Article
- An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus.Nature cell biology · 2023Article
- GKLOMLI: a link prediction model for inferring miRNA-lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm.BMC bioinformatics · 2023Article
- Migration/Differentiation-Associated LncRNAGenes · 2022Article
- HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis.Molecular therapy. Nucleic acids · 2022Article
- Manipulation of the miR-378a/mt-ATP6 regulatory axis rescues ATP synthase in the diabetic heart and offers a novel role for lncRNA Kcnq1ot1.American journal of physiology. Cell physiology · 2022Article
- The lncRNAs/miR-30e/CHI3L1 Axis Is Dysregulated in Systemic Sclerosis.Biomedicines · 2022Article
- Review
- AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity.Scientific reports · 2021Article
- Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells.Cancers · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Argonaute crosslinking and immunoprecipitation (CLIP) experiments are the most widely used high-throughput methodologies for miRNA targetome characterization. The analysis of Photoactivatable Ribonucleoside-Enhanced (PAR) CLIP methodology focuses on sequence clusters containing T-to-C conversions. Here, we demonstrate for the first time that the non-T-to-C clusters, frequently observed in PAR-CLIP experiments, exhibit functional miRNA-binding events and strong RNA accessibility. This discovery is based on the analysis of an extensive compendium of bona fide miRNA-binding events, and is further supported by numerous miRNA perturbation experiments and structural sequencing data. The incorporation of these previously neglected clusters yields an average of 14% increase in miRNA-target interactions per PAR-CLIP library. Our findings are integrated in microCLIP ( www.microrna.gr/microCLIP ), a cutting-edge framework that combines deep learning classifiers under a super learning scheme. The increased performance of microCLIP in CLIP-Seq-guided detection of miRNA interactions, uncovers previously elusive regulatory events and miRNA-controlled pathways.
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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.