.png){kind=icon}
返回
Cell clustering for spatial transcriptomics data with graph neural networks
.png){kind=icon}
PRE
AI
DOI：10.1038/s43588-022-00266-5.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
Spatial transcriptomics data can provide high-throughput gene expression profiling and the spatial structure of tissues simultaneously. Most studies have relied on only the gene expression information but cannot utilize the spatial information efficiently. Taking advantage of spatial transcriptomics and graph neural networks, we introduce cell clustering for spatial transcriptomics data with graph neural networks, an unsupervised cell clustering method based on graph convolutional networks to improve ab initio cell clustering and discovery of cell subtypes based on curated cell category annotation. On the basis of its application to five in vitro and in vivo spatial datasets, we show that cell clustering for spatial transcriptomics outperforms other spatial clustering approaches on spatial transcriptomics datasets and can clearly identify all four cell cycle phases from multiplexed error-robust fluorescence in situ hybridization data of cultured cells. From enhanced sequential fluorescence in situ hybridization data of brain, cell clustering for spatial transcriptomics finds functional cell subtypes with different micro-environments, which are all validated experimentally, inspiring biological hypotheses about the underlying interactions among the cell state, cell type and micro-environment.
Keyword:
GENE-EXPRESSION
期刊
IF:
18.3
论文数:
3.1K
被引数:
4.0K
机构
引用论文
Spatial organization of the somatosensory cortex revealed by osmFISHosmFISH揭示的体感皮层的空间组织.png)
NATURE METHODS
NATURE METHODSIF32.1
PREAI
分享收藏CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid TissuesCytoMAP: 空间分析工具箱揭示淋巴组织中髓样细胞组织的特征CELL REPORTS
OAAI
CELL REPORTSIF6.9
OAAI分享收藏MALAT1 promotes cell proliferation in gastric cancer by recruiting SF2/ASFMALAT1通过募集SF2/ASF促进胃癌细胞增殖OAAI
OAAI分享收藏From Louvain to Leiden: guaranteeing well-connected communities从鲁汶到莱顿: 保证良好连接的社区SCIENTIFIC REPORTSOAAI
SCIENTIFIC REPORTSIF3.9
OAAI分享收藏High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization具有多重错误的高通量单细胞基因表达谱-稳健的荧光原位杂交OAAI
OAAI分享收藏Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profilingNATURE COMMUNICATIONSOAAI
NATURE COMMUNICATIONSIF15.7
OAAI分享收藏Binding of a 4-Methyl-4-Aza-Steroid to 5α-Reductase of Rat Liver and Prostate Microsomes4-甲基-4-氮杂-类固醇与大鼠肝脏和前列腺微粒体的5 α-还原酶的结合
PREAI
分享收藏
查看更多内容