ArticlePLoS genetics2018
regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation.Briefings in bioinformatics · 2026Article
- Regulatory QTLs affecting miRNA-mRNA interactions in cancer: mechanisms, methods, and clinical implications.Frontiers in molecular biosciences · 2025Review
- Genetic Variants ofGenes · 2022Article
- Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.BMC genomic data · 2022Article
- Article
- A novel regQTL-SNP and the risk of lung cancer: a multi-dimensional study.Archives of toxicology · 2021Article
- Methylation and expression levels of microRNA-23b/-24-1/-27b, microRNA-30c-1/-30e, microRNA-301a and let-7g are dysregulated in clear cell renal cell carcinoma.Molecular biology reports · 2021Article
- Article
- Multiplex-Heterogeneous Network-Based Capturing Potential SNP "Switches" of Pathways Associating With Diverse Disease Characteristics of Asthma.Frontiers in cell and developmental biology · 2021Article
- Association of KLK3, VAMP8 and MDM4 Genetic Variants within microRNA Binding Sites with Prostate Cancer: Evidence from Serbian Population.Pathology oncology research : POR · 2020Article
- Critical Analysis of Genome-Wide Association Studies: Triple Negative Breast CancerInternational journal of molecular sciences · 2020Review
- The miR-146a SNP Rs2910164 and miR-155 SNP rs767649 Are Risk Factors for Non-Small Cell Lung Cancer in the Iranian Population.Canadian respiratory journal · 2020Article
- Two-stage Bayesian GWAS of 9576 individuals identifies SNP regions that are targeted by miRNAs inversely expressed in Alzheimer's and cancer.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2020Article
- The role of dietary phytochemicals in the carcinogenesis via the modulation of miRNA expression.Journal of cancer research and clinical oncology · 2019Review
- An 8 miRNA-Based Risk Score System for Predicting the Prognosis of Patients With Papillary Thyroid Cancer.Technology in cancer research & treatmentArticle
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet their functional properties often remain unclear. It has been hypothesized that SNPs in microRNA binding sites may disrupt gene regulation by microRNAs (miRNAs), short non-coding RNAs that bind to mRNA and downregulate the target gene. While several studies have predicted the location of SNPs in miRNA binding sites, to date there has been no comprehensive analysis of their impact on miRNA regulation. Here we investigate the functional properties of genetic variants and their effects on miRNA regulation of gene expression in cancer. Our analysis is motivated by the hypothesis that distinct alleles may cause differential binding (from miRNAs to mRNAs or from transcription factors to DNA) and change the expression of genes. We previously identified pathways-systems of genes conferring specific cell functions-that are dysregulated by miRNAs in cancer, by comparing miRNA-pathway associations between healthy and tumor tissue. We draw on these results as a starting point to assess whether SNPs on dysregulated pathways are responsible for miRNA dysregulation of individual genes in tumors. Using an integrative regression analysis that incorporates miRNA expression, mRNA expression, and SNP genotype data, we identify functional SNPs that we term "regulatory QTLs (regQTLs)": loci whose alleles impact the regulation of genes by miRNAs. We apply the method to breast, liver, lung, and prostate cancer data from The Cancer Genome Atlas, and provide a tool to explore the findings.
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