Cell type prioritization in single-cell data

被引：127

作者：

Skinnider, Michael A. ^{[1
,2
]}

Squair, Jordan W. ^{[1
,3
,4
,5
]}

Kathe, Claudia ^{[1
,3
,4
]}

Anderson, Mark A. ^{[1
,3
,4
]}

Gautier, Matthieu ^{[1
,3
,4
]}

Matson, Kaya J. E. ^{[6
]}

Milano, Marco ^{[1
,3
,4
]}

Hutson, Thomas H. ^{[1
,3
,4
]}

Barraud, Quentin ^{[1
,3
,4
]}

Phillips, Aaron A. ^{[7
,8
,9
,10
]}

Foster, Leonard J. ^{[2
,11
]}

La Manno, Gioele ^{[1
]}

Levine, Ariel J. ^{[6
]}

Courtine, Gregoire ^{[1
,3
,4
,12
]}

机构：

[1] Ecole Polytech Fed Lausanne EPFL, Fac Life Sci, Brain Mind Inst, Lausanne, Switzerland

[2] Univ British Columbia, Michael Smith Labs, Vancouver, BC, Canada

[3] Lausanne Univ Hosp CHUV, Dept Clin Neurosci, NeuroRestore, Lausanne, Switzerland

[4] Univ Lausanne UNIL, Lausanne, Switzerland

[5] Univ British Columbia, Int Collaborat Repair Discoveries ICORD, Vancouver, BC, Canada

[6] NINDS, Spinal Circuits & Plast Unit, Bldg 36,Rm 4D04, Bethesda, MD 20892 USA

[7] Univ Calgary, Cumming Sch Med, Hotchkiss Brain Inst, Dept Physiol & Pharmacol, Calgary, AB, Canada

[8] Univ Calgary, Cumming Sch Med, Hotchkiss Brain Inst, Dept Clin Neurosci, Calgary, AB, Canada

[9] Univ Calgary, Cumming Sch Med, Hotchkiss Brain Inst, Dept Cardiac Sci, Calgary, AB, Canada

[10] Univ Calgary, Cumming Sch Med, Libin Cardiovasc Inst Alberta, Calgary, AB, Canada

[11] Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC, Canada

[12] Ecole Polytech Fed Lausanne EPFL, Fac Life Sci, Ctr Neuroprosthet, Lausanne, Switzerland

来源：

NATURE BIOTECHNOLOGY | 2021年 / 39卷 / 01期

基金：

瑞士国家科学基金会; 欧洲研究理事会; 加拿大健康研究院;

关键词：

GENE-EXPRESSION; ARCHITECTURE; DEFINES; ENABLES; ATLAS; NOISE;

D O I：

10.1038/s41587-020-0605-1

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We present Augur, a method to prioritize the cell types most responsive to biological perturbations in single-cell data. Augur employs a machine-learning framework to quantify the separability of perturbed and unperturbed cells within a high-dimensional space. We validate our method on single-cell RNA sequencing, chromatin accessibility and imaging transcriptomics datasets, and show that Augur outperforms existing methods based on differential gene expression. Augur identified the neural circuits restoring locomotion in mice following spinal cord neurostimulation. The cell types affected by biological perturbations in complex tissues are uncovered by single-cell analysis.

引用

页码：30 / 34

页数：5

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