Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
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DOI：
10.1038/s41467-022-30755-0
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发表时间：
2022-06-09
影响因子：
16.6
通讯作者：
中科院分区：
文献类型：
--
作者：
随着单细胞数据，特别是转录学数据的日益普及，人们对细胞间通讯的推断产生了越来越大的兴趣。为此开发了许多计算工具。它们中的每一个都由细胞间相互作用的先验知识资源和预测潜在的细胞间通信事件的方法组成。然而，资源和方法的选择对结果预测的影响在很大程度上是未知的。为了阐明这一点，我们系统地比较了16种细胞间通信推理资源和7种方法，以及这些方法之间的预测一致性。在这些资源中，我们发现很少有独特的相互作用，不同程度的重叠，以及对特定途径和组织丰富蛋白的不均匀覆盖。然后，我们研究了所有可能的方法和资源组合，并表明两者都强烈影响预测的细胞间相互作用。最后，我们评估了细胞-细胞通讯方法与空间共定位、细胞因子活性和受体蛋白丰度的一致性，并发现预测通常与这些数据模式一致。为了便于使用本工作中描述的方法和资源，我们提供了Liana，一个配体-受体分析框架，作为所有资源和方法的开源接口。目前有多种从单个小区数据推断小区间通信(CCC)的方法可用。在这里，作者系统地比较了16种CCC推理资源和7种方法，并开发了Liana框架作为接口来使用和比较所有这些方法。
The growing availability of single-cell data, especially transcriptomics, has sparked an increased interest in the inference of cell-cell communication. Many computational tools were developed for this purpose. Each of them consists of a resource of intercellular interactions prior knowledge and a method to predict potential cell-cell communication events. Yet the impact of the choice of resource and method on the resulting predictions is largely unknown. To shed light on this, we systematically compare 16 cell-cell communication inference resources and 7 methods, plus the consensus between the methods’ predictions. Among the resources, we find few unique interactions, a varying degree of overlap, and an uneven coverage of specific pathways and tissue-enriched proteins. We then examine all possible combinations of methods and resources and show that both strongly influence the predicted intercellular interactions. Finally, we assess the agreement of cell-cell communication methods with spatial colocalisation, cytokine activities, and receptor protein abundance and find that predictions are generally coherent with those data modalities. To facilitate the use of the methods and resources described in this work, we provide LIANA, a LIgand-receptor ANalysis frAmework as an open-source interface to all the resources and methods. Multiple methods to infer cell-cell communication (CCC) from single cell data are currently available. Here, the authors systematically compare 16 CCC inference resources and 7 methods, and develop the LIANA framework as an interface to use and compare all these approaches.
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影响因子：
5.8
作者：
Gu, Zuguang;Eils, Roland;Schlesner, Matthias
通讯作者：
Schlesner, Matthias
影响因子：
--
作者：
Fazekas D;Koltai M;Türei D;Módos D;Pálfy M;Dúl Z;Zsákai L;Szalay-Bekő M;Lenti K;Farkas IJ;Vellai T;Csermely P;Korcsmáros T
通讯作者：
Korcsmáros T
影响因子：
48
作者：
Browaeys, Robin;Saelens, Wouter;Saeys, Yvan
通讯作者：
Saeys, Yvan
影响因子：
14.8
作者：
Efremova, Mirjana;Vento-Tormo, Miquel;Vento-Tormo, Roser
通讯作者：
Vento-Tormo, Roser
DOI：
10.1126/stke.2003.187.re9
发表时间：
2003-06-17
期刊：
Science's STKE : signal transduction knowledge environment
影响因子：
--
作者：
Ben-Shlomo, Izhar;Yu Hsu, Sheau;Hsueh, Aaron J W
通讯作者：
Hsueh, Aaron J W