Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology.

ABSTRACT: The rapid growth of large-scale spatial gene expression data demands efficient and reliable computational tools to extract major trends of gene expression in their native spatial context. Here, we used stability-driven unsupervised learning (i.e., staNMF) to identify principal patterns (PPs) of 3D gene expression profiles and understand spatial gene distribution and anatomical localization at the whole mouse brain level. Our subsequent spatial correlation analysis systematically compared the PPs to known anatomical regions and ontology from the Allen Mouse Brain Atlas using spatial neighborhoods. We demonstrate that our stable and spatially coherent PPs, whose linear combinations accurately approximate the spatial gene data, are highly correlated with combinations of expert-annotated brain

SUBMITTER: Cahill R 

PROVIDER: S-EPMC11406299 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature