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- W4310155347 abstract "The rapidly developing spatial omics generated datasets with diverse scales and modalities. However, most existing methods focus on modeling dynamics of single cells while ignore microenvironments (MEs). Here we present SOTIP (Spatial Omics mulTIPle-task analysis), a versatile method incorporating MEs and their interrelationships into a unified graph. Based on this graph, spatial heterogeneity quantification, spatial domain identification, differential microenvironment analysis, and other downstream tasks can be performed. We validate each module's accuracy, robustness, scalability and interpretability on various spatial omics datasets. In two independent mouse cerebral cortex spatial transcriptomics datasets, we reveal a gradient spatial heterogeneity pattern strongly correlated with the cortical depth. In human triple-negative breast cancer spatial proteomics datasets, we identify molecular polarizations and MEs associated with different patient survivals. Overall, by modeling biologically explainable MEs, SOTIP outperforms state-of-art methods and provides some perspectives for spatial omics data exploration and interpretation." @default.
- W4310155347 created "2022-11-30" @default.
- W4310155347 creator A5026020173 @default.
- W4310155347 creator A5028378330 @default.
- W4310155347 creator A5037767553 @default.
- W4310155347 creator A5046695536 @default.
- W4310155347 creator A5058814283 @default.
- W4310155347 creator A5060480375 @default.
- W4310155347 creator A5089823903 @default.
- W4310155347 date "2022-11-28" @default.
- W4310155347 modified "2023-10-14" @default.
- W4310155347 title "SOTIP is a versatile method for microenvironment modeling with spatial omics data" @default.
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