ArticleNucleic acids research2013
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Acid bile salt induces esophageal mucosal barrier dysfunction through miR-146a-5p-KYNU pathway in gastroesophageal reflux disease.Esophagus : official journal of the Japan Esophageal Society · 2026Article
- An efficient framework to decipher microRNA regulatory programs applied to T cells.Genes and immunity · 2025Article
- Evaluating Genetic Regulators of MicroRNAs Using Machine Learning Models.International journal of molecular sciences · 2025Article
- MicroRNAs in atrial fibrillation target genes in structural remodelling.Cell and tissue research · 2023Article
- Magnetique: an interactive web application to explore transcriptome signatures of heart failure.Journal of translational medicine · 2022Article
- New Tricks with Old Dogs: Computational Identification and Experimental Validation of New miRNA-mRNA Regulation in hiPSC-CMs.Biomedicines · 2022Article
- Huntington's disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization.The Journal of clinical investigation · 2021Article
- miRTissueBMC bioinformatics · 2020Article
- miR‑144‑3p inhibits the proliferation, migration and angiogenesis of multiple myeloma cells by targeting myocyte enhancer factor 2A.International journal of molecular medicine · 2020Article
- Transcriptome Characterization of Repressed Embryonic Myogenesis Due to Maternal Calorie Restriction.Frontiers in cell and developmental biology · 2020Article
- Investigating gene-microRNA networks in atrial fibrillation patients with mitral valve regurgitation.PloS one · 2020Article
- mRNA and miRNA expression profiles in an ectoderm-biased substate of human pluripotent stem cells.Scientific reports · 2019Article
- A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes.BMC genomics · 2019Article
- miRTissue: a web application for the analysis of miRNA-target interactions in human tissues.BMC bioinformatics · 2018Article
- miR-148a and miR-17-5p synergistically regulate milk TAG synthesis via PPARGC1A and PPARA in goat mammary epithelial cells.RNA biology · 2017Article
- Integration of microRNA and mRNA expression profiles in the skin of systemic sclerosis patients.Scientific reports · 2017Article
- Article
- Gene Expression Differences in Prostate Cancers between Young and Old Men.PLoS genetics · 2016Article
- Exocytosis of polyubiquitinated proteins in bortezomib-resistant leukemia cells: a role for MARCKS in acquired resistance to proteasome inhibitors.Oncotarget · 2016Article
- Integrating multidimensional omics data for cancer outcome.Biostatistics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current microRNA target predictions are based on sequence information and empirically derived rules but do not make use of the expression of microRNAs and their targets. This study aimed to improve microRNA target predictions in a given biological context, using in silico predictions, microRNA and mRNA expression. We used target prediction tools to produce lists of predicted targets and used a gene set test designed to detect consistent effects of microRNAs on the joint expression of multiple targets. In a single test, association between microRNA expression and target gene set expression as well as the contribution of the individual target genes on the association are determined. The strongest negatively associated mRNAs as measured by the test were prioritized. We applied our integration method to a well-defined muscle differentiation model. Validation of our predictions in C2C12 cells confirmed predicted targets of known as well as novel muscle-related microRNAs. We further studied associations between microRNA-mRNA pairs in human prostate cancer, finding some pairs that have been recently experimentally validated by others. Using the same study, we showed the advantages of the global test over Pearson correlation and lasso. We conclude that our integrated approach successfully identifies regulated microRNAs and their targets.
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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.