Biological process activity transformation of single cell gene expression for cross-species alignment

Hongxu Ding; Andrew Blair; Ying Yang; Joshua M Stuart

doi:10.1038/s41467-019-12924-w

Biological process activity transformation of single cell gene expression for cross-species alignment

Nat Commun. 2019 Oct 25;10(1):4899. doi: 10.1038/s41467-019-12924-w.

Authors

Hongxu Ding¹, Andrew Blair², Ying Yang³, Joshua M Stuart⁴

Affiliations

¹ Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA. hding16@ucsc.edu.
² Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
³ Department of Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA.
⁴ Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA. jstuart@ucsc.edu.

Abstract

The maintenance and transition of cellular states are controlled by biological processes. Here we present a gene set-based transformation of single cell RNA-Seq data into biological process activities that provides a robust description of cellular states. Moreover, as these activities represent species-independent descriptors, they facilitate the alignment of single cell states across different organisms.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Computational Biology / methods*
Gene Expression
Gene Expression Profiling / methods*
Gene Expression Regulation, Developmental / genetics
Humans
Leukocytes, Mononuclear / metabolism
Mice
Mouse Embryonic Stem Cells / metabolism
Sequence Analysis, RNA / methods*
Signal-To-Noise Ratio
Single-Cell Analysis / methods
Systems Biology
Zebrafish / genetics

Abstract

Publication types

MeSH terms

Grants and funding