InterCellDB: A User-Defined Database for Inferring Intercellular Networks.
InterCellDB: A User-Defined Database for Inferring Intercellular Networks.
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InterCellDB：用于推断细胞间网络的用户定义数据库
DOI：
10.1002/advs.202200045
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发表时间：
2022-08
期刊：
影响因子：
15.1
通讯作者：
Shi, Ligen
中科院分区：
文献类型：
--
作者：
Jin, Ziyang;Zhang, Xiaotao;Dai, Xuejiao;Huang, Jinyan;Hu, Xiaoming;Zhang, Jianmin;Shi, Ligen
单细胞RNA测序（scRNA-seq）的最新进展使人们能够深入了解特定组织内的细胞间串扰。然而，可定制的数据分析工具，从基因表达与生物学功能破译细胞间通信是缺乏的。作者开发了InterCellDB，这是一个允许使用scRNA-seq数据集结合蛋白质注释信息（包括细胞定位和功能分类以及蛋白质相互作用特性）进行用户定义的细胞间通信分析的平台。InterCellDB在肿瘤微环境研究中的应用使用来自人类和小鼠的两个独立的scRNA-seq数据集来举例说明，并证明InterCellDB推断的细胞-细胞相互作用和配体-受体对是实验有效的。用户自定义分析：开发了一个平台，用于使用单细胞RNA测序（scRNA-seq）数据集对细胞间串扰进行用户定义的分析。蛋白质注释包括表达变化、细胞定位和功能分类。蛋白质相互作用的属性，包括证据来源，可信度得分，行动模式，行动效果。因此，可以通过InterCellDB进一步探索生物学上有意义的过程。
Recent advances in single cell RNA sequencing (scRNA‐seq) empower insights into cell–cell crosstalk within specific tissues. However, customizable data analysis tools that decipher intercellular communication from gene expression in association with biological functions are lacking. The authors have developed InterCellDB, a platform that allows a user‐defined analysis of intercellular communication using scRNA‐seq datasets in combination with protein annotation information, including cellular localization and functional classification, and protein interaction properties. The application of InterCellDB in tumor microenvironment research is exemplified using two independent scRNA‐seq datasets from human and mouse and it is demonstrated that InterCellDB‐inferred cell–cell interactions and ligand–receptor pairs are experimentally valid. User‐defined analysis: A platform is developed for user‐defined analysis on intercellular crosstalk using single cell RNA sequencing (scRNA‐seq) datasets. Protein annotation including expression change, cellular localization and functional classification are considered. Protein interaction properties including evidence source, credibility score, action mode, and action effect are provided as well. Therefore, biological meaningful processes can be explored further by InterCellDB.
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影响因子：
14.9
作者：
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通讯作者：
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