ArticleNature communications2025
ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Logistic regression for estimating functional effects with spatial transcriptomics.Nucleic acids research · 2026Article
- Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics.Nature communications · 2026Article
- Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity.bioRxiv : the preprint server for biology · 2025Article
- ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics.Nature communications · 2025Article
- Statistical and computational methods for enabling the clinical and translational application of spatial transcriptomics.Clinical and translational medicine · 2024Article
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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 protein-coding mRNAs, while cytoplasmic- or membrane-enriched genes frequently encode ribosomal proteins or contain signal peptides. ELLA also uncovers dynamic subcellular localization changes across the cell cycle. Overall, ELLA is a powerful, robust, and scalable tool for subcellular spatial expression analysis across high-resolution spatial transcriptomics platforms.
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