ArticlePLoS computational biology2012
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 40 citations in OpenAlex.
- Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species.MicroRNA (Shariqah, United Arab Emirates) · 2024Review
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- miR-488-5p promotes esophageal squamous cell carcinoma progression by suppressing the P53 pathway.Journal of thoracic disease · 2021Article
- MicroRNA-10a Negatively Regulates CD4Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs.BMC bioinformatics · 2020Article
- miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19Frontiers in cellular and infection microbiology · 2020Article
- RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets.BMC bioinformatics · 2019Article
- Identified the Synergistic Mechanism ofEvidence-based complementary and alternative medicine : eCAM · 2019Article
- Obesity-induced mitochondrial dysfunction in porcine adipose tissue-derived mesenchymal stem cells.Journal of cellular physiology · 2018Article
- Assigning function to natural allelic variation via dynamic modeling of gene network induction.Molecular systems biology · 2018Article
- Hypoxia-related microRNA-210 is a diagnostic marker for discriminating osteoblastoma and osteosarcoma.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2017Article
- MicroRNA screening identifies a link between NOVA1 expression and a low level of IKAP in familial dysautonomia.Disease models & mechanisms · 2016Article
- Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies.PloS one · 2016Article
- Sexually dimorphic effects of gestational endocrine-disrupting chemicals on microRNA expression in the developing rat hypothalamus.Molecular and cellular endocrinology · 2015Article
- RNA sequencing reveals a depletion of collagen targeting microRNAs in Dupuytren's disease.BMC medical genomics · 2015Article
- SubmiRine: assessing variants in microRNA targets using clinical genomic data sets.Nucleic acids research · 2015Article
- Aldosterone regulates microRNAs in the cortical collecting duct to alter sodium transport.Journal of the American Society of Nephrology : JASN · 2014Article
- Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach.Nucleic acids research · 2014Article
- Let-7d microRNA affects mesenchymal phenotypic properties of lung fibroblasts.American journal of physiology. Lung cellular and molecular physiology · 2014Article
- Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways.Journal of molecular and cellular cardiology · 2013Article
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that bind to their target mRNAs through base complementarity. Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictions. Until recently, very few algorithms considered the dynamic nature of the interactions, including the effect of less specific interactions, the miRNA expression level, and the effect of combinatorial miRNA binding. Addressing these issues can result in a more accurate miRNA:mRNA modeling with many applications, including efficient miRNA-related SNP evaluation. We present a novel thermodynamic model based on the Fermi-Dirac equation that incorporates miRNA expression in the prediction of target occupancy and we show that it improves the performance of two popular single miRNA target finders. Modeling combinatorial miRNA targeting is a natural extension of this model. Two other algorithms show improved prediction efficiency when combinatorial binding models were considered. ComiR (Combinatorial miRNA targeting), a novel algorithm we developed, incorporates the improved predictions of the four target finders into a single probabilistic score using ensemble learning. Combining target scores of multiple miRNAs using ComiR improves predictions over the naïve method for target combination. ComiR scoring scheme can be used for identification of SNPs affecting miRNA binding. As proof of principle, ComiR identified rs17737058 as disruptive to the miR-488-5p:NCOA1 interaction, which we confirmed in vitro. We also found rs17737058 to be significantly associated with decreased bone mineral density (BMD) in two independent cohorts indicating that the miR-488-5p/NCOA1 regulatory axis is likely critical in maintaining BMD in women. With increasing availability of comprehensive high-throughput datasets from patients ComiR is expected to become an essential tool for miRNA-related studies.
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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.