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Ma A, Wang X, Li J, Wang C, Xiao T, Liu Y, Cheng H, Wang J, Li Y, Chang Y, Li J, Wang D, Jiang Y, Su L, Xin G, Gu S, Li Z, Liu B, Xu D, Ma Q. Single-cell biological network inference using a heterogeneous graph transformer. Nat Commun 2023; 14:964. [PMID: 36810839 PMCID: PMC9944243 DOI: 10.1038/s41467-023-36559-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities simultaneously to capture the intricacy of complex molecular mechanisms and cellular heterogeneity. Existing tools cannot effectively infer the active biological networks in diverse cell types and the response of these networks to external stimuli. Here we present DeepMAPS for biological network inference from scMulti-omics. It models scMulti-omics in a heterogeneous graph and learns relations among cells and genes within both local and global contexts in a robust manner using a multi-head graph transformer. Benchmarking results indicate DeepMAPS performs better than existing tools in cell clustering and biological network construction. It also showcases competitive capability in deriving cell-type-specific biological networks in lung tumor leukocyte CITE-seq data and matched diffuse small lymphocytic lymphoma scRNA-seq and scATAC-seq data. In addition, we deploy a DeepMAPS webserver equipped with multiple functionalities and visualizations to improve the usability and reproducibility of scMulti-omics data analysis.
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Affiliation(s)
- Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaoying Wang
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Jingxian Li
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Cankun Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yuntao Liu
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Hao Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Yang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Yuzhou Chang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jinpu Li
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Yuexu Jiang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Li Su
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Gang Xin
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Shaopeng Gu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, China.
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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