Distribution-free screening of spatially variable genes in spatial transcriptomics
Fuente:
arXiv
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Preprint |
| Published: |
2026
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866914380802686976 |
|---|---|
| author | Wang, Changhu Huang, Qiyun Chen, Zihao Liu, Jin Xi, Ruibin |
| author_facet | Wang, Changhu Huang, Qiyun Chen, Zihao Liu, Jin Xi, Ruibin |
| contents | Spatial transcriptomics (ST) technologies enable transcriptome-wide gene expression profiling while preserving spatial resolution, offering unprecedented opportunities to uncover complex spatial structures. Due to the ultra-high dimensionality of ST data, identifying spatially variable genes (SVGs) associated with unknown spatial clusters has become a central task in ST data analysis. Here, we develop a distribution-free SVG screening method based on a novel quasi-likelihood ratio statistic, the MM-test, combined with a knockoff procedure to control the false discovery rate (FDR). MM-test leverages auxiliary information, such as spatial distances, about the unknown spatial domains for SVG screening. Notably, in addition to two-dimensional ST datasets, MM-test is well-suited for increasingly common three-dimensional (3D), multi-slice ST datasets. Extensive benchmarking using simulations and 34 real ST datasets demonstrates that MM-test consistently outperforms existing SVG detection methods. In a 3D mouse brain dataset, MM-test accurately delineates fine-scale structures that are challenging for other methods, such as the 3D architecture of the pyramidal layer of the hippocampal cornu ammonis and the dentate gyrus. Theoretical guarantees-including selection consistency, FDR control, and an error bound for post-selection clustering-are also established. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2603_09061 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Distribution-free screening of spatially variable genes in spatial transcriptomics Wang, Changhu Huang, Qiyun Chen, Zihao Liu, Jin Xi, Ruibin Applications Methodology Spatial transcriptomics (ST) technologies enable transcriptome-wide gene expression profiling while preserving spatial resolution, offering unprecedented opportunities to uncover complex spatial structures. Due to the ultra-high dimensionality of ST data, identifying spatially variable genes (SVGs) associated with unknown spatial clusters has become a central task in ST data analysis. Here, we develop a distribution-free SVG screening method based on a novel quasi-likelihood ratio statistic, the MM-test, combined with a knockoff procedure to control the false discovery rate (FDR). MM-test leverages auxiliary information, such as spatial distances, about the unknown spatial domains for SVG screening. Notably, in addition to two-dimensional ST datasets, MM-test is well-suited for increasingly common three-dimensional (3D), multi-slice ST datasets. Extensive benchmarking using simulations and 34 real ST datasets demonstrates that MM-test consistently outperforms existing SVG detection methods. In a 3D mouse brain dataset, MM-test accurately delineates fine-scale structures that are challenging for other methods, such as the 3D architecture of the pyramidal layer of the hippocampal cornu ammonis and the dentate gyrus. Theoretical guarantees-including selection consistency, FDR control, and an error bound for post-selection clustering-are also established. |
| title | Distribution-free screening of spatially variable genes in spatial transcriptomics |
| topic | Applications Methodology |
| url | https://arxiv.org/abs/2603.09061 |