ArticleHuman genomics2021
High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis.
Article in Human genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Role of Tumor Debulking Surgery in Improving Survival of Patients with Head and Neck Cancer: A Systematic Review.Current oncology (Toronto, Ont.) · 2026Pooled it
- HopRatio: Profiling single-sample transcriptomic dysregulation using stable gene-ordering relationships.iScience · 2026Article
- Identifying molecular signatures of parapneumonic effusion reveals HMGB2 as the disease progression biomarker.Respiratory research · 2026Article
- multiDEGGs: Single or Multiomic Differential Network Analysis for Biomarker Discovery and Feature Engineering for Predictive Modeling.Computational and structural biotechnology journal · 2026Article
- Identification of disease-specific regulatory networks in prurigo nodularis versus atopic dermatitis through ATAC/RNA single-nucleus profiling.The Journal of allergy and clinical immunology · 2025Article
- Network-based approach identifies key genes associated with tumor heterogeneity in HPV positive and negative head and neck cancer patients.Scientific reports · 2025Article
- Elevated Methylation Contributes to Suppressed Expression of Special AT-Rich Sequence-Binding Protein 2 in Colorectal Cancer: A Gene-Disease Association Study.Health science reports · 2025Article
- Integrated multi-sample transcriptomic analysis of COVID-19 patients against controls using a bioinformatics pipeline.Scientific reports · 2025Article
- RNA-Seq Study of Human Lens Epithelial Cells: Differentially Expressed Genes and Pathways in Steroid, Uveitic, Post-Vitrectomy, and Senile Cataracts.Investigative ophthalmology & visual science · 2025Article
- Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes.PLoS computational biology · 2025Article
- Resistance signatures manifested in early drug response across cancer types and species.Cancer drug resistance (Alhambra, Calif.) · 2025Article
- Integrative analysis of bulk and single-cell RNA sequencing data reveals increased arachidonic acid metabolism in osteoarthritic chondrocytes.Frontiers in medicine · 2025Article
- Unlocking reproducible transcriptomic signatures for acute myeloid leukaemia: Integration, classification and drug repurposing.Journal of cellular and molecular medicine · 2024Article
- Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.iScience · 2024Article
- Static magnetic field-induced IL-6 secretion in periodontal ligament stem cells accelerates orthodontic tooth movement.Scientific reports · 2024Article
- lncRNA-mRNA Co-Expression and Regulation Analysis in Lung Fibroblasts from Idiopathic Pulmonary Fibrosis.Non-coding RNA · 2024Article
- Radiotranscriptomics of non-small cell lung carcinoma for assessing high-level clinical outcomes using a machine learning-derived multi-modal signature.Biomedical engineering online · 2023Article
- Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets.Genome biology · 2023Review
- N-of-one differential gene expression without control samples using a deep generative model.Genome biology · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible.
resultsOur findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis.
conclusionsHigh heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.