Uncovering cell identity through differential stability with Cepo

Hani Jieun Kim; Kevin Wang; Carissa Chen; Yingxin Lin; Patrick P L Tam; David M Lin; Jean Y H Yang; Pengyi Yang

doi:10.1038/s43588-021-00172-2

Uncovering cell identity through differential stability with Cepo

Nat Comput Sci. 2021 Dec;1(12):784-790. doi: 10.1038/s43588-021-00172-2. Epub 2021 Dec 20.

Authors

Hani Jieun Kim^{1

2

3}, Kevin Wang¹, Carissa Chen^{2

3}, Yingxin Lin^{1

3}, Patrick P L Tam^{4

5}, David M Lin⁶, Jean Y H Yang^{1

3}, Pengyi Yang^{7

8

9

10}

Affiliations

¹ School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia.
² Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia.
³ Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
⁴ Embryology Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia.
⁵ School of Medical Science, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.
⁶ Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.
⁷ School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia. pengyi.yang@sydney.edu.au.
⁸ Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia. pengyi.yang@sydney.edu.au.
⁹ Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia. pengyi.yang@sydney.edu.au.
¹⁰ School of Medical Science, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia. pengyi.yang@sydney.edu.au.

PMID: 38217190
DOI: 10.1038/s43588-021-00172-2

Abstract

The use of single-cell RNA-sequencing (scRNA-seq) allows observation of different cells at multi-tiered complexity in the same microenvironment. To get insights into cell identity using scRNA-seq data, we present Cepo, which generates cell-type-specific gene statistics of differentially stable genes from scRNA-seq data to define cell identity. When applied to multiple datasets, Cepo outperforms current methods in assigning cell identity and enhances several cell identification applications such as cell-type characterisation, spatial mapping of single cells and lineage inference of single cells.

Abstract

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