ArticlePloS one2013
Effects of sample size on differential gene expression, rank order and prediction accuracy of a gene signature.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 2 of them syntheses that pooled it.
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Who cites it
37 citing papers in PubMed, 2 syntheses or guidelines pooled it, 67 citations in OpenAlex.
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- Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies.BMC neurology · 2017Pooled it
- A standardized randomized 6-month aerobic exercise-training down-regulated pro-inflammatory genes, but up-regulated anti-inflammatory, neuron survival and axon growth-related genes.Experimental gerontology · 2015Trial
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- Integrating Network Pharmacology, Machine Learning, and Experimental Validation to Elucidate the Mechanism of Cardamonin in Treating Idiopathic Pulmonary Fibrosis.International journal of molecular sciences · 2025Article
- Reduced ZMPSTE24 expression leads to prelamin accumulation and development of steatosis in MASLD patients.Scientific reports · 2025Article
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- Acute promyelocytic leukemia withOncology letters · 2024Article
- GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis.Patterns (New York, N.Y.) · 2024Article
- Skeletal muscle omics signatures in cancer cachexia: perspectives and opportunities.Journal of the National Cancer Institute. Monographs · 2023Article
- Cross-species predictive modeling reveals conserved drought responses between maize and sorghum.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Expression and clinical significance of undifferentiated embryonic cell transcription factor 1 in breast cancer.Translational cancer research · 2023Article
- Skeletal Muscle Transcriptomic Comparison Between Men and Women in Response to Acute Sprint Exercise.Frontiers in genetics · 2022Article
- Characterizing theTherapeutic advances in medical oncology · 2022Article
- SOX2 and Bcl-2 as a Novel Prognostic Value in Hepatocellular Carcinoma Progression.Current oncology (Toronto, Ont.) · 2021Article
- PathExt: a general framework for path-based mining of omics-integrated biological networks.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Top differentially expressed gene lists are often inconsistent between studies and it has been suggested that small sample sizes contribute to lack of reproducibility and poor prediction accuracy in discriminative models. We considered sex differences (69♂, 65 ♀) in 134 human skeletal muscle biopsies using DNA microarray. The full dataset and subsamples (n = 10 (5 ♂, 5 ♀) to n = 120 (60 ♂, 60 ♀)) thereof were used to assess the effect of sample size on the differential expression of single genes, gene rank order and prediction accuracy. Using our full dataset (n = 134), we identified 717 differentially expressed transcripts (p<0.0001) and we were able predict sex with ~90% accuracy, both within our dataset and on external datasets. Both p-values and rank order of top differentially expressed genes became more variable using smaller subsamples. For example, at n = 10 (5 ♂, 5 ♀), no gene was considered differentially expressed at p<0.0001 and prediction accuracy was ~50% (no better than chance). We found that sample size clearly affects microarray analysis results; small sample sizes result in unstable gene lists and poor prediction accuracy. We anticipate this will apply to other phenotypes, in addition to sex.
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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.