SynthesisNature communications2025
Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis.
Synthesis in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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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.
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Who cites it
4 citing papers in PubMed.
- Reduced expression of Brain Expressed X-linked genes in Alzheimer's disease.Journal of Alzheimer's disease : JAD · 2026Article
- Coordinated dysregulation of modular gene activity in human neuropathologies.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic Meta-Analysis as a Framework for Robust Cross-Study Biological Inference.International journal of molecular sciences · 2026Review
- An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.Genome biology · 2026Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
False positive claims of differentially expressed genes (DEGs) in scRNA-seq studies are of substantial concern. We found that DEGs from individual Parkinson's (PD), Huntington's (HD), and COVID-19 datasets had moderate predictive power for case-control status of other datasets, but DEGs from Alzheimer's (AD) and Schizophrenia (SCZ) datasets had poor predictive power. We developed a non-parametric meta-analysis method, SumRank, based on reproducibility of relative differential expression ranks across datasets, and found DEGs with improved predictive power. Specificity and sensitivity of these genes were substantially higher than those discovered by dataset merging and inverse variance weighted p-value aggregation methods. Up-regulated DEGs implicated chaperone-mediated protein processing in PD glia and lipid transport in AD and PD microglia, while down-regulated DEGs were in glutamatergic processes in AD astrocytes and excitatory neurons and synaptic functioning in HD FOXP2 neurons. Lastly, we evaluate factors influencing reproducibility of individual studies as a prospective guide for experimental design.
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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 Socratic graph.