Work

A Comparison of Cell-Cell Interaction Prediction Tools Based on scRNA-seq Data

Year: 2023

Type: article

Abstract: Computational prediction of cell-cell interactions (CCIs) is becoming increasingly important for understanding disease development and progression. We present a benchmark study of available CCI prediction tools based on single-cell RNA sequencing (scRNA-seq) data. By comparing prediction outputs with a manually curated gold standard for idiopathic pulmonary fibrosis (IPF), we evaluated prediction performance and processing time of several CCI prediction tools, including CCInx, CellChat, CellPhoneDB, iTALK, NATMI, scMLnet, SingleCellSignalR, and an ensemble of tools. According to our results, CellPhoneDB and NATMI are the best performer CCI prediction tools, among the ones analyzed, when we define a CCI as a source-target-ligand-receptor tetrad. In addition, we recommend specific tools according to different types of research projects and discuss the possible future paths in the field.

Source: Biomolecules

DOI: 10.3390/biom13081211

Authors: Zihong Xie, Xuri Li, Antonio Mora

Institutions: Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,558