CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.
CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.
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CellNeighborEX：从空间转录数据中破译依赖邻居的基因表达。
DOI：
10.15252/msb.202311670
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发表时间：
2023-11-09
影响因子：
9.9
通讯作者：
Won, Kyoung Jae
中科院分区：
文献类型：
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作者：
Kim, Hyobin;Kumar, Amit;Lovkvist, Cecilia;Palma, Antonio M.;Martin, Patrick;Kim, Junil;Bhoopathi, Praveen;Trevino, Jose;Fisher, Paul;Madan, Esha;Gogna, Rajan;Won, Kyoung Jae
Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor‐dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing further insight. We found that cells express different genes depending on their neighboring cell types in various tissues including mouse embryos, brain, and liver cancer. Those genes are associated with critical biological processes such as development or metastases. We further validated that gene expression is induced by neighboring partners via spatial visualization. The neighbor‐dependent gene expression suggests new potential genes involved in cell–cell interactions beyond what ligand‐receptor co‐expression can discover. CellNeighborEX is a computational tool for exploring transcriptomic changes caused by direct cell contact in spatial transcriptomics data. CellNeighborEX provides a new perspective on cellular communication between two adjacent cells.
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影响因子：
64.8
作者：
Cao, Junyue;Spielmann, Malte;Shendure, Jay
通讯作者：
Shendure, Jay
DOI：
10.1073/pnas.2205371120
发表时间：
2023-01-10
影响因子：
11.1
作者：
通讯作者：
--
影响因子：
46.9
作者：
Giladi, Amir;Cohen, Merav;Amit, Ido
通讯作者：
Amit, Ido
影响因子：
48
作者：
Browaeys, Robin;Saelens, Wouter;Saeys, Yvan
通讯作者：
Saeys, Yvan
影响因子：
64.5
作者：
Cho CS;Xi J;Si Y;Park SR;Hsu JE;Kim M;Jun G;Kang HM;Lee JH
通讯作者：
Lee JH