A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes.

ABSTRACT: We assessed the reproducibility of differentially expressed genes (DEGs) in previously published Alzheimer's (AD), Parkinson's (PD), Huntington's (HD), Schizophrenia (SCZ), and COVID-19 scRNA-seq studies. While transcriptional scores from DEGs of individual PD, HD, and COVID-19 datasets had moderate predictive power for case-control status of other datasets, genes from individual AD and 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. By multiple metrics, specificity and sensitivity of these genes were substantially higher than those discovered by dataset merging and inverse variance weighted p-value aggregati

SUBMITTER: Nakatsuka N 

PROVIDER: S-EPMC11507907 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature