Protocol for unsupervised inference of cell-cell communication using matrix decomposition
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Updated: Jun 28, 2025
A Rapid, Scalable Method for the Isolation, Functional Study, and Analysis of Cell-derived Extracellular Matrix
Published on: January 4, 2017
Yi Liu1, Xiao Chang2, Xiaoping Liu3
1Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
Abstract:
Exploring cell-cell communication is pivotal for understanding biological processes in multicellular life forms. Here, we present a protocol that details the use of matrix decomposition to infer cell-cell communication (MDIC3) for unsupervised cell-cell communication inference. We describe steps for using the MDIC3 Python scripts to deduce cell-cell communication and identify key ligand-receptor pairs between a specific cell type pair from a single-cell gene expression dataset. This protocol has potential application in cell-cell communication inference on any species. For complete details on the use and execution of this protocol, please refer to Liu et al.1.
