Fokker-Planck diffusion maps of microglial transcriptomes reveal radial differentiation into substates associated with Alzheimer's pathology.

ABSTRACT: The identification of microglia subtypes is important for understanding the role of innate immunity in neurodegenerative diseases. Current methods of unsupervised cell type identification assume a small noise-to-signal ratio of transcriptome measurements to produce well-separated cell clusters. However, identification of subtypes can be obscured by gene expression noise, which diminishes the distances in transcriptome space between distinct cell types, blurs boundaries, and reduces reproducibility. Here we use Fokker-Planck (FP) diffusion maps to model cellular differentiation as a stochastic process whereby cells settle into local minima that correspond to cell subtypes, in a potential landscape constructed from transcriptome data using a nearest neighbor graph approach. By applying criti

SUBMITTER: Baumgartner A 

PROVIDER: S-EPMC11846988 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature