CellDialog: A Computational Framework for Ligand-Receptor-Mediated Cell-Cell Communication Analysis
Lihong Peng, Wei Xiong, Chendi Han, Zejun Li, Xing Chen
Abstract
Intercellular communication significantly influences tumor progression, metastasis, and therapy resistance. An intercellular communication inference method includes two main procedures: ligand-receptor interaction (LRI) curation and LRI-mediated intercellular communication strength measurement. The construction of a comprehensive, high-confident and well-organized LRI database contributes to intercellular communication inference. Here, we developed a computational framework named CellDialog to reconstruct an intercellular connectivity network based on the combined expression of ligands and receptors involved in sender and receiver cells. CellDialog first captures high-confident LRIs through LRI feature extraction, feature selection, and classification. Furthermore, CellDialog uses a three-point estimation approach to measure the LRI-mediated intercellular communication strength by combining LRI filtering and single-cell RNA sequencing data. A comparison analysis of CellDialog and the other tools was conducted, and it was found that CellDialog can efficiently decode intercellular communications. Additionally, CellDialog offers a heatmap view and network view for intercellular communication visualization. In summary, CellDialog provides a tool that allows researchers to analyze intercellular signal transduction. It is freely available at https://github.com/plhhnu/CellDialog.