Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
Open accessAbstract
mirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score. The algorithm trains a regression model on sequence and contextual features extracted from miRanda-predicted target sites. In a large-scale evaluation, miRanda-mirSVR is competitive with other target prediction methods in identifying target genes and predicting the extent of their downregulation at the mRNA or protein levels. Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites.
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Predicted targets of microRNA-137 were significantly enriched for dURVs (OR=1.13; 95% CI=1.09-1.18; P=6.8e-4).
“Predicted targets of microRNA-13736, previously identified as localized near common SNPs associated with schizophrenia37, were also significantly enriched for dURVs (OR=1.13; 95% CI=1.09–1.18; P = 6.8 × 10−4) (Fig. 2).”
From Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia (2016) · cites this paper as [36]
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- Authors
- Betel, D., Koppal, A., Agius, P., Sander, C., & Leslie, C.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Columbia University (US)
- Corresponding author
- Leslie, Christina
- Venue
- Genome Biology
- Published
- 2010-08-27
- Volume
- 11
- Issue
- 8
- Pages
- R90-R90
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC2945792
- OpenAlex
- W2041509376
- Cited by
- 1,592
- References
- 39
- Citations by year
- 2026: 30 · 2025: 49 · 2024: 75 · 2023: 60 · 2022: 121 · 2021: 110 · 2020: 143 · 2019: 121 · 2018: 143 · 2017: 162 · 2016: 128 · 2015: 118 · 2014: 114 · 2013: 103 · 2012: 72
- FWCI
- 21.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (U24CA143840)
- National Institute of General Medical Sciences (P01GM073047)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- microRNA binding sites, Miranda
- MeSH terms
- Algorithms, Artificial Intelligence, Binding Sites, Models, Molecular, Proteins, Regression Analysis, RNA, Messenger, Down-Regulation, MicroRNAs
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