DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data

Abstract

Detecting changes in gene coordination patterns between biological conditions and identifying the cell populations in which these changes occur are key challenges in single-cell analysis. Existing approaches often compare gene co-expression between predefined cell clusters or rely on aligning cells across conditions. These strategies can be suboptimal when changes occur within small subpopulations or when batch effects obscure the underlying biological signal. To address these challenges, we introduce DiCoLo, a framework that identifies genes exhibiting differential co-localization, defined as changes in coordinated expression within localized cell neighborhoods-subsets of highly similar cells in the transcriptomic space. Importantly, DiCoLo does not rely on cell clustering or cross-condition alignment. For each condition, DiCoLo constructs a gene graph using Optimal Transport distances that reflect gene co-localization patterns across the cell manifold. Then, it identifies differential gene programs by detecting changes in connectivity patterns between the gene graphs. We show that DiCoLo robustly identifies differential gene co-localization even under weak signals or complex batch effects, outperforming existing methods across multiple benchmark datasets. When applied to mouse hair follicle development data, DiCoLo reveals coordinated gene programs and emerging cell populations driven by perturbations in morphogen signaling that underlie dermal condensate differentiation. Overall, these results establish DiCoLo as a powerful framework for uncovering localized differential transcriptional coordinated patterns in single-cell data.