ArticleBMC bioinformatics2009
Data-driven normalization strategies for high-throughput quantitative RT-PCR.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 2 of them syntheses that pooled it.
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Who cites it
67 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies.PloS one · 2015Pooled it
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- Prediction of treatment response to adalimumab: a double-blind placebo-controlled study of circulating microRNA in patients with early rheumatoid arthritis.The pharmacogenomics journal · 2016Trial
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- Associations between telomere length, glucocorticoid receptor gene DNA methylation, volume of stress-related brain structures, and academic performance in middle-school-age children.Comprehensive psychoneuroendocrinology · 2024Article
- Normalizing real-time PCR results in routine testing.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue.Genome biology · 2023Article
- miRNome expression analysis in canine diffuse large B-cell lymphoma.Frontiers in oncology · 2023Article
- Serum miRNA modulations indicate changes in retinal morphology.Frontiers in molecular neuroscience · 2023Article
- Evidence for Effects of Extracellular Vesicles on Physical, Inflammatory, Transcriptome and Reward Behaviour Status in Mice.International journal of molecular sciences · 2022Article
- qPCRtools: An R package for qPCR data processing and visualization.Frontiers in genetics · 2022Article
- Comparison of Data Normalization Strategies for Array-Based MicroRNA Profiling Experiments and Identification and Validation of Circulating MicroRNAs as Endogenous Controls in Hypertension.Frontiers in genetics · 2022Article
- Predicting clinical events using Bayesian multivariate linear mixed models with application to scleroderma.BMC medical research methodology · 2021Article
- A novel wastewater-based epidemiology indexing method predicts SARS-CoV-2 disease prevalence across treatment facilities in metropolitan and regional populations.Scientific reports · 2021Article
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- Carotid sinus nerve stimulation attenuates alveolar bone loss and inflammation in experimental periodontitis.Scientific reports · 2020Article
- Evaluation of a modified method of extraction, purification, and characterization of lipopolysaccharide (O antigen) fromVeterinary world · 2020Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
backgroundHigh-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage technology allows the acquisition of profiles for a moderate number of genes (50 to a few thousand), and this number continues to grow. The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline.
resultsWe present and evaluate two data-driven normalization methods that directly correct for technical variation and represent robust alternatives to standard housekeeping gene-based approaches. We evaluated the performance of these methods against a single gene housekeeping gene method and our results suggest that quantile normalization performs best. These methods are implemented in freely-available software as an R package qpcrNorm distributed through the Bioconductor project.
conclusionThe utility of the approaches that we describe can be demonstrated most clearly in situations where standard housekeeping genes are regulated by some experimental condition. For large qPCR-based data sets, our approaches represent robust, data-driven strategies for normalization.
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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.