.png){kind=icon}
返回
SOTIP is a versatile method for microenvironment modeling with spatial omics data
.png){kind=icon}
OA
AI
DOI：10.1038/s41467-022-34867-5.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
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. Methods that analyse heterogeneity and compare tissue microenvironments using spatial omics data are challenging to develop. Here, the authors present SOTIP, a method that can perform spatial heterogeneity, spatial domain, and differential microenvironment analyses across multiple spatial omics modalities.
Keyword:
TISSUE
SEQ
ARCHITECTURE
EXPRESSION
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
IF:
15.7
论文数:
9.4W
被引数:
91.2W
机构
引用论文
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface空间分辨转录组学揭示了肿瘤-微环境界面的结构.png)
NATURE COMMUNICATIONSOAAI
NATURE COMMUNICATIONSIF15.7
OAAI分享收藏The immunological and metabolic landscape in primary and metastatic liver cancerNATURE REVIEWS CANCER
NATURE REVIEWS CANCERIF66.8
PREAI
分享收藏Spatial organization of the somatosensory cortex revealed by osmFISHosmFISH揭示的体感皮层的空间组织NATURE METHODS
NATURE METHODSIF32.1
PREAI
分享收藏
查看更多内容