ArticleGenome biology2022
Exaggerated false positives by popular differential expression methods when analyzing human population samples.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 papers, 2 of them syntheses that pooled it.
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Who cites it
185 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders.PloS one · 2023Pooled it
- Tumor microenvironment biomarkers predicting pathological response to neoadjuvant chemoimmunotherapy in locally advanced esophageal squamous cell carcinoma: post-hoc analysis of a single center, phase 2 study.Journal for immunotherapy of cancer · 2024Trial
- The RNA cargo of plasma-derived extracellular vesicles in mCRPC patients captures cancer cells and tumor microenvironment signals.bioRxiv : the preprint server for biology · 2026Article
- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- DEAPLOG: Differential Expression Analysis and Pseudo-Temporal Locating and Ordering of Genes in Single-Cell Transcriptomic Data.Interdisciplinary sciences, computational life sciences · 2026Article
- SIEVEseq: unified differential expression, variability, and skewness analyses using RNA-Seq data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Network-based machine learning to identify biomarkers for systemic lupus erythematosus.BMC biology · 2026Article
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- Differential transcriptomic landscapes of olive cultivars facing Xylella fastidiosa infection.BMC plant biology · 2026Article
- AWmeta Empowers Adaptively Weighted Transcriptomic Meta-Analysis.Current issues in molecular biology · 2026Article
- Statistical knockoffs improve biomarker discovery from transcriptomic data.Briefings in bioinformatics · 2026Article
- SLC22A3 deficiency leads to cognitive impairment through the cardio-neuroinflammatory axis mediated HA/H1R/NLRP3 pathway in heart failure mice.Redox biology · 2026Article
- BET1 serves as a prognostic indicator and promotes cancer proliferation in glioblastoma multiforme.Discover oncology · 2026Article
- Transcriptomic analysis in autism spectrum disorder suggests three molecular subtypes with distinct phenotypic profiles and functional pathways.Communications biology · 2026Article
- Investigation of molecular immune regulation mechanisms and therapeutic target prediction in pancreatic cancer based on bioinformatics and genetics.Clinics (Sao Paulo, Brazil) · 2026Article
- Functional Portability of a Hyperaccumulator-Derived Core Microbiome: Enhancing Cadmium Phytoextraction inToxics · 2026Article
- Cardiometabolic adaptations in the cave nectar bat Eonycteris spelaea.Communications biology · 2026Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
125 more citing papers are in PubMed but not listed here.
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Abstract
When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates. Expanding the analysis to limma-voom, NOISeq, dearseq, and Wilcoxon rank-sum test, we found that FDR control is often failed except for the Wilcoxon rank-sum test. Particularly, the actual FDRs of DESeq2 and edgeR sometimes exceed 20% when the target FDR is 5%. Based on these results, for population-level RNA-seq studies with large sample sizes, we recommend the Wilcoxon rank-sum test.
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