Robust and adaptive non-parametric tests for detecting general distributional shifts in gene expression

Abstract

Differential expression analysis is crucial in genomics, yet most methods focus only on mean shifts. Variance shifts in gene expression-especially in cellular signaling and aging-are increasingly recognized as being biologically important. We present QRscore (quantile rank score), a general non-parametric framework that extends the Mann-Whitney test to detect both mean and variance shifts through model-informed weights derived from negative binomial (NB) and zero-inflated NB (ZINB) distributions. QRscore offers high statistical power with false discovery rate (FDR) control, surpassing existing methods in detecting both types of distributional changes. When applied to bulk RNA sequencing (RNA-seq) data from Genotype-Tissue Expression (GTEx), QRscore uncovers numerous genes with dispersion shifts that are missed by mean-shift analysis. In pseudo-bulked single-cell RNA-seq data from the Asian Immune Diversity Atlas (AIDA), QRscore further reveals cell-type-specific variance shifts across age groups that remain undetectable in bulk analyses. QRscore augments the genome bioinformatics toolkit by offering a powerful and flexible approach for differential expression analysis.

Keywords: CP: Computational biology; CP: Systems biology; RNA-seq analysis; aging; differential dispersion; differential expression; pseudo-bulk single-cell analysis; statistical hypothesis testing.