Table 2 Definitions of concepts for SVGs and frequentist statistical tests
| Â | Concept | Definition |
|---|---|---|
SVGs | Overall SVGs | Genes that exhibit non-random spatial expression patterns. This is the most general category of SVGs detected using only SRT data without incorporating external information such as spatial domains or cell types. |
| Â | Cell-type-specific SVGs | Genes that exhibit non-random spatial expression patterns within a cell type. These genes are detected using both SRT data and external cell-type annotations for the spatial spots. |
| Â | Spatial-domain-marker SVGs | Genes that exhibit significantly higher expression in a spatial domain compared to other domains. These genes are detected using SRT data and spatial domains, which are usually detected from the same SRT data. |
Frequentist tests | Dependent test | Examines the dependence between a gene’s expression level and the spatial location. |
|  | Fixed-effect tests | Examines whether some or all of the fixed-effect covariates xi contribute to the mean of the response variable, i.e., a gene’s expression. |
|  | Random-effect tests | Examines whether the random-effect covariates zi contribute to the variance of the response variable, i.e., a gene’s expression. |
