Kernel-Based Testing for Single-Cell Differential Analysis
This work addresses the problem of detecting subtle population variations in single-cell analysis for researchers in genomics and bioinformatics, representing an incremental improvement over traditional methods.
The paper tackles the challenge of comparing molecular feature distributions in single-cell data by proposing a kernel-testing framework for non-linear cell-wise distribution comparison, applied to gene expression and epigenomic modifications, which identifies untreated breast cancer cells with an epigenomic profile resembling persister cells.
Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and epigenomic modifications. Our method allows feature-wise and global transcriptome/epigenome comparisons, revealing cell population heterogeneities. Using a classifier based on embedding variability, we identify transitions in cell states, overcoming limitations of traditional single-cell analysis. Applied to single-cell ChIP-Seq data, our approach identifies untreated breast cancer cells with an epigenomic profile resembling persister cells. This demonstrates the effectiveness of kernel testing in uncovering subtle population variations that might be missed by other methods.