ArticleScientific reports2017
Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 221 papers.
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Who cites it
221 citing papers in PubMed.
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- Transcriptomic Analysis IdentifiesAnimals : an open access journal from MDPI · 2026Article
- Mitochondrial Abundant Heat Soluble (MAHS) Protein Expression Modulates Metabolic Dynamics in Human Adipose-Derived Stem Cells.International journal of molecular sciences · 2026Article
- Integrated Study of Vancomycin-Induced Nephrotoxicity in the Context of Sepsis: Animal Models and Transcriptomics.Kidney360 · 2026Article
- Comparative Analysis of Quorum Sensing-Dependent Transcriptomic Responses in Phytopathogenic Burkholderia spp.The plant pathology journal · 2026Article
- Comparative Analysis of Heat Exposure-Induced Molecular Changes in Two Turtle Species with Contrasting Thermal Adaptations.Integrative zoology · 2026Article
- Dynamic interplay of maternal and paternal contributions to offspring phenotype in Eurasian perch.BMC biology · 2026Article
- Transcriptome-Based WGCNA Reveals Hub Genes Involved in Copper Resistance ofInternational journal of molecular sciences · 2026Article
- Functional profiling of somatostatin receptors identifies somatostatin receptor subtype 2 as a vulnerability in Succinate Dehydrogenase SDHB-deficient pheochromocytomas and paragangliomas.Molecular biomedicine · 2026Article
- Rejuvenation of mesenchymal stromal cells via partial reprogramming enables scalable generation of transcriptionally diverse MSC libraries.Stem cell research & therapy · 2026Article
- An RNA interference biopesticide reduces reproduction of the honey bee parasite Varroa destructor by down-regulating embryo development pathways.Pest management science · 2026Article
- Fetal programming of the cardiac mitochondrial permeability transition pore in male offspring from hypoxic pregnancies.Redox biology · 2026Article
- Zhuyu pill relieves cholestasis in rats by modulating the expression of lncRNAs and circRNAs.Frontiers in pharmacology · 2026Article
- A study exploring the effects of exercise on cuproptosis targets in Alzheimer's disease brains based on large-scale data.Archives of medical science : AMS · 2026Article
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161 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene counts from sequencing reads. While a number of benchmarking studies have been conducted, the question remains how individual methods perform at accurately quantifying gene expression levels from RNA-sequencing reads. We performed an independent benchmarking study using RNA-sequencing data from the well established MAQCA and MAQCB reference samples. RNA-sequencing reads were processed using five workflows (Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq, Kallisto and Salmon) and resulting gene expression measurements were compared to expression data generated by wet-lab validated qPCR assays for all protein coding genes. All methods showed high gene expression correlations with qPCR data. When comparing gene expression fold changes between MAQCA and MAQCB samples, about 85% of the genes showed consistent results between RNA-sequencing and qPCR data. Of note, each method revealed a small but specific gene set with inconsistent expression measurements. A significant proportion of these method-specific inconsistent genes were reproducibly identified in independent datasets. These genes were typically smaller, had fewer exons, and were lower expressed compared to genes with consistent expression measurements. We propose that careful validation is warranted when evaluating RNA-seq based expression profiles for this specific gene set.
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