ArticlePloS one2014
Normalization of RNA-sequencing data from samples with varying mRNA levels.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Review
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- Extracellular Vesicles from Animal Milk: Great Potentialities and Critical Issues.Animals : an open access journal from MDPI · 2022Review
- Transcriptome Profiling of Starvation in the Peripheral Chemosensory Organs of the Crop PestInsects · 2021Article
- Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA.Nature communications · 2021Article
- Gene expression profile of human follicle dermal papilla cells in response to Camellia japonica phytoplacenta extract.FEBS open bio · 2021Article
- Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction.Scientific reports · 2020Article
- Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols.RNA (New York, N.Y.) · 2020Review
- Article
- BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers.Nucleic acids research · 2020Article
- Prediction and Characterization of miRNA/Target Pairs in Non-Model Plants Using RNA-seq.Current protocols in plant biology · 2019Article
- Unanchored ubiquitin chains do not lead to marked alterations in gene expression inBiology open · 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
- Smooth quantile normalization.Biostatistics (Oxford, England) · 2018Article
- Article
- Serum MicroRNAs Reflect Injury Severity in a Large Animal Model of Thoracic Spinal Cord Injury.Scientific reports · 2017Article
- Article
- Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model.PLoS pathogens · 2016Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Methods for normalization of RNA-sequencing gene expression data commonly assume equal total expression between compared samples. In contrast, scenarios of global gene expression shifts are many and increasing. Here we compare the performance of three normalization methods when polyA(+) RNA content fluctuates significantly during zebrafish early developmental stages. As a benchmark we have used reverse transcription-quantitative PCR. The results show that reads per kilobase per million (RPKM) and trimmed mean of M-values (TMM) normalization systematically leads to biased gene expression estimates. Biological scaling normalization (BSN), designed to handle differences in total expression, showed improved accuracy compared to the two other methods in estimating transcript level dynamics. The results have implications for past and future studies using RNA-sequencing on samples with different levels of total or polyA(+) RNA.
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