ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics.

ABSTRACT: Spatial transcriptomics technologies are becoming increasingly high-resolution, enabling gene expression measurement at the subcellular level. Here, we present subcellular expression localization analysis (ELLA), a statistical framework for modeling subcellular mRNA localization and detecting spatially variable genes within cells. ELLA uses an over-dispersed nonhomogeneous Poisson process to model spatial count data with a unified cellular coordinate system to anchor diverse cellular morphologies, demonstrating effective type I error control and high power in simulations. In real data applications, ELLA identifies genes with distinct subcellular localization and associate these patterns to key mRNA characteristics: nuclear-enriched genes exhibit an abundance of long noncoding RNAs or prote

SUBMITTER: Wang JX 

PROVIDER: S-EPMC12606177 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature