ArticleNucleic acids research2014
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Investigate synergistic and competitive regulation between miRNAs by using a multivariate information measurement.BMC bioinformatics · 2026Article
- Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler.Cell genomics · 2023Article
- Article
- Review
- Computing microRNA-gene interaction networks in pan-cancer using miRDriver.Scientific reports · 2022Article
- Recognizing and stabilizing miR-21 by chiral ruthenium(II) complexes.BMC chemistry · 2020Article
- Robust edge-based biomarker discovery improves prediction of breast cancer metastasis.BMC bioinformatics · 2020Article
- ASDmiR: A Stepwise Method to Uncover miRNA Regulation Related to Autism Spectrum Disorder.Frontiers in genetics · 2020Article
- A Survey of Regulatory Interactions Among RNA Binding Proteins and MicroRNAs in Cancer.Frontiers in genetics · 2020Article
- Altered microRNA and target gene expression related to Tetralogy of Fallot.Scientific reports · 2019Article
- Comprehensive Analysis of Human microRNA-mRNA Interactome.Frontiers in genetics · 2019Article
- TDP-43 regulates cancer-associated microRNAs.Protein & cell · 2018Article
- Integrated Analysis of MicroRNA (miRNA) and mRNA Profiles Reveals Reduced Correlation between MicroRNA and Target Gene in Cancer.BioMed research international · 2018Article
- A path-based measurement for human miRNA functional similarities using miRNA-disease associations.Scientific reports · 2016Article
- Review
- Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods.Cancer informatics · 2016Review
- Predicting miRNA Targets by Integrating Gene Regulatory Knowledge with Expression Profiles.PloS one · 2016Article
- Article
- c-myc in whitefish (Coregonus lavaretus): structure, expression, and insights into possible posttranscriptional regulatory mechanism.Fish physiology and biochemistry · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aberrant microRNA (miRNA) expression is implicated in tumorigenesis. The underlying mechanisms are unclear because the regulations of each miRNA on potentially hundreds of mRNAs are sample specific. We describe a novel approach to infer Probabilistic MiRNA-mRNA Interaction Signature ('ProMISe') from a single pair of miRNA-mRNA expression profile. Our model considers mRNA and miRNA competition as a probabilistic function of the expressed seeds (matches). To demonstrate ProMISe, we extensively exploited The Cancer Genome Atlas data. As a target predictor, ProMISe identifies more confidence/validated targets than other methods. Importantly, ProMISe confers higher cancer diagnostic power than using expression profiles alone. Gene set enrichment analysis on averaged ProMISe uniquely revealed respective target enrichments of oncomirs miR-21 and 145 in glioblastoma and ovarian cancers. Moreover, comparing matched breast (BRCA) and thyroid (THCA) tumor/normal samples uncovered thousands of tumor-related interactions. For example, ProMISe-BRCA network involves miR-155/183/21, which exhibits higher ProMISe coupled with coherently higher miRNA expression and lower target expression; oncomirs miR-221/222 in the ProMISe-THCA network engage with many downregulated target genes. Together, our probabilistic approach of integrating expression and sequence scores establishes a functional link between the aberrant miRNA and mRNA expression, which was previously under-appreciated due to the methodological differences.
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