ArticleRNA (New York, N.Y.)2013
The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 69 citations in OpenAlex.
- Proposal of supervised data analysis strategy of plasma miRNAs from hybridisation array data with an application to assess hemolysis-related deregulation.BMC bioinformatics · 2015Trial
- Fluorescent hydrogel kit based on photonic crystal-enhanced DNA-templated silver nanoclusters for miRNA detection.Analytical and bioanalytical chemistry · 2026Article
- Double-Flapped Dumbbell Probe Functionalized with Silver Nanoclusters for Sensitive Fluorometric Detection of miRNA.Applied biochemistry and biotechnology · 2025Article
- Exonuclease-III Assisted Signal Cycle Integrating with Self-Priming Mediated Chain Extension for Sensitive and Reliable MicroRNA Detection.ACS omega · 2025Article
- MiR-223-3p in Cancer Development and Cancer Drug Resistance: Same Coin, Different Faces.International journal of molecular sciences · 2024Review
- A simple and efficient strategy for trace detection of ferroptosis-related miRNAs based on novel hydrophobic paper-based plasmonic substrate and "inverse molecular sentinel (iMS)" nanoprobes.Frontiers in bioengineering and biotechnology · 2023Article
- Induction of Apoptosis and Regulation of MicroRNA Expression by (2Molecules (Basel, Switzerland) · 2021Article
- Dynamic mRNP Remodeling in Response to Internal and External Stimuli.Biomolecules · 2020Review
- Metabolite-mediated TOR signaling regulates the circadian clock inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes.BMC genomics · 2019Article
- Normalization Methods for the Analysis of Unbalanced Transcriptome Data: A Review.Frontiers in bioengineering and biotechnology · 2019Review
- Bayesian multilevel model of micro RNA levels in ovarian-cancer and healthy subjects.PloS one · 2019Article
- c-Myc is a novelThe Journal of biological chemistry · 2018Article
- Selection of reference genes for miRNA qRT-PCR under abiotic stress in grapevine.Scientific reports · 2018Article
- Modified Polyadenylation-Based RT-qPCR Increases Selectivity of Amplification of 3'-MicroRNA Isoforms.Frontiers in genetics · 2018Article
- Stress-induced changes in miRNA biogenesis and functioning.Cellular and molecular life sciences : CMLS · 2018Review
- Analysis of microRNA Expression Profiles Induced by Yiqifumai Injection in Rats with Chronic Heart Failure.Frontiers in physiology · 2018Article
- Quantum Dot Based Nano-Biosensors for Detection of Circulating Cell Free miRNAs in Lung Carcinogenesis: From Biology to Clinical Translation.Frontiers in genetics · 2018Review
- Methods and novel technology for microRNA quantification in colorectal cancer screening.Clinical epigenetics · 2017Review
- Circulating MicroRNAs As Potential Biomarkers for Veterinary Infectious Diseases.Frontiers in veterinary science · 2017Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have established that mutations or deletions in microRNA (miRNA) processing enzymes resulting in a global decrease of miRNA expression are frequent across cancers and can be associated with a poorer prognosis. While very popular in miRNA profiling studies, it remains unclear whether miRNA microarrays are suited or not to accurately detecting global miRNA decreases seen in cancers. In this work, we analyzed the miRNA profiles of samples with global miRNA decreases using Affymetrix miRNA microarrays following the inducible genetic deletion of Dicer1. Surprisingly, up to a third of deregulated miRNAs identified upon Dicer1 depletion were found to be up-regulated following standard robust multichip average (RMA) background correction and quantile normalization, indicative of normalization bias. Our comparisons of five preprocess steps performed at the probe level demonstrated that the use of cyclic loess relying on non-miRNA small RNAs present on the Affymetrix platform significantly improved specificity and sensitivity of detection of decreased miRNAs. These findings were validated in samples from patients with prostate cancer, where conjugation of robust normal-exponential background correction with cyclic loess normalization and array weights correctly identified the greatest number of decreased miRNAs, and the lowest amount of false-positive up-regulated miRNAs. These findings highlight the importance of miRNA microarray normalization for the detection of miRNAs that are truly differentially expressed and suggest that the use of cyclic loess based on non-miRNA small RNAs can help to improve the sensitivity and specificity of miRNA profiling in cancer samples with global miRNA decrease.
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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.