ArticleFrontiers in plant science2018
Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size.
Article in Frontiers in plant science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
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- High-throughput phenotypic screening identifies the phytochemical melissic acid that mitigates SHED cellular senescence via the ADCY5/cAMP/CREB axis.Frontiers in pharmacology · 2026Article
- SCAMP3-Driven Regulation of ERK1/2 and Autophagy Phosphoproteomics Signatures in Triple-Negative Breast Cancer.International journal of molecular sciences · 2025Article
- Proteomics Integrated with Transcriptomics of Clubroot Resistant and SusceptibleInternational journal of molecular sciences · 2025Article
- AI-Enhanced Transcriptomic Discovery of Druggable Targets and Repurposed Therapies for Huntington's Disease.Brain sciences · 2025Review
- Chemical, morphological, and genetic characterization of the floral scent and scent-releasing structures of Gynandropsis gynandra (Cleomaceae, Brassicales).Plant biology (Stuttgart, Germany) · 2025Article
- LincRNA-MSTRG.673.2 Promotes Chicken Intramuscular Adipocyte Differentiation by Sponging miR-128-3p.Animals : an open access journal from MDPI · 2025Article
- Hypoxanthine activates PI3K/AKT pathway and lipid metabolism, hallmarks in breast cancer metastasis.Medical oncology (Northwood, London, England) · 2025Article
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Article
- Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes.PLoS computational biology · 2025Article
- High-resolution transcriptional impact of AIRE: effects of pathogenic variants p.Arg257Ter, p.Cys311Tyr, and polygenic risk variant p.Arg471Cys.Frontiers in immunology · 2025Article
- The variegatedComputational and structural biotechnology journal · 2024Article
- Transcriptome Analysis of Human Dermal Cells Infected with Candida auris Identified Unique Pathogenesis/Defensive Mechanisms Particularly Ferroptosis.Mycopathologia · 2024Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo.eLife · 2024Article
- miR-128-3p inhibits intramuscular adipocytes differentiation in chickens by downregulating FDPS.BMC genomics · 2023Article
- Considerations for reproducible omics in aging research.Nature aging · 2023Review
- Article
Corrections and comments
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Authors and funding
9 authors.
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Abstract
RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. While the main drawback of previous relevant studies is the lack of generality, we conducted both an analysis of a two-condition experiment (with eight biological replicates per condition) to compare the results with previous benchmark studies, and a meta-analysis of 17 experiments with up to 18 biological conditions, eight biological replicates and 100 million (M) reads per sample. As a global trend, we concluded that the replicate number has a larger impact than the library size on the power of the DE analysis, except for low-expressed genes, for which both parameters seem to have the same impact. Our study also provides new insights for practitioners aiming to enhance their experimental designs. For instance, by analyzing both the sensitivity and specificity of the DE analysis, we showed that the optimal threshold to control the false discovery rate (FDR) is approximately 2
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