Alignment of single-cell trajectories to compare cellular expression dynamics
Abstract
Single-cell RNA sequencing and high-dimensional cytometry can be used to generate detailed trajectories of dynamic biological processes such as differentiation or development. Here we present cellAlign, a quantitative framework for comparing expression dynamics within and between single-cell trajectories. By applying cellAlign to mouse and human embryonic developmental trajectories, we systematically delineate differences in the temporal regulation of gene expression programs that would otherwise be masked.
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We now detect genes that vary across a trajectory by regressing gene expression against pseudotime.
“While early approaches to find trajectory‐associated genes involved DE testing between cell clusters along a trajectory (Haghverdi et al, 2016; Alpert et al, 2018), we now detect genes that vary across a trajectory by regressing gene expression against pseudotime.”
From Current best practices in single-cell RNA-seq analysis: a tutorial (2019) · cites this paper as Alpert et al, 2018
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Current best practices in single-cell RNA-seq analysis: a tutorial
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- Authors
- Alpert, A., Moore, L. S., Dubovik, T., & Shen-Orr, S. S.
- Affiliations
- Technion – Israel Institute of Technology (IL)
- Corresponding author
- Shen-Orr, Shai S
- ORCID
- Shen-Orr, Shai S
- Venue
- Nature Methods
- Published
- 2018-03-12
- Volume
- 15
- Issue
- 4
- Pages
- 267-270
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2789661952
- Cited by
- 96
- References
- 13
- Citations by year
- 2026: 6 · 2025: 12 · 2024: 15 · 2023: 10 · 2022: 3 · 2021: 19 · 2020: 8 · 2019: 16 · 2018: 7
- FWCI
- 4.44
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- single-cell RNA sequencing, mass cytometry, gene expression dynamics, embryonic development, cell differentiation, temporal gene regulation, high-dimensional cytometry, mouse embryo, human embryo
- MeSH terms
- Animals, Base Sequence, Cytophotometry, Gene Expression Regulation, Humans, Sequence Analysis, RNA, Mice, Single-Cell Analysis, Transcriptome
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