Diffusion pseudotime robustly reconstructs lineage branching

被引：814

作者：

Haghverdi, Laleh ^{[1
,2
]}

Buettner, Maren ^{[1
]}

Wolf, F. Alexander ^{[1
]}

Buettner, Florian ^{[1
,3
]}

Theis, Fabian J. ^{[1
,2
]}

机构：

[1] Helmholtz Zentrum Munchen, Inst Computat Biol, German Res Ctr Environm Hlth, Neuherberg, Germany

[2] Tech Univ Munich, Dept Math, Munich, Germany

[3] European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge, England

来源：

NATURE METHODS | 2016年 / 13卷 / 10期

基金：

英国医学研究理事会;

关键词：

RNA-SEQUENCING DATA; SINGLE-CELL DATA; EXPRESSION; HETEROGENEITY; TRAJECTORIES; PROGRESSION; COMMITMENT; EMBRYO; MAPS; STEM;

D O I：

10.1038/nmeth.3971

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.

引用

页码：845 / +

页数：6

共 20 条

[1]

destiny: diffusion maps for large-scale single cell data in R [J].

Angerer, Philipp ;

Haghverdi, Laleh ;

Buettner, Maren ;

Theis, Fabian J. ;

Marr, Carsten ;

Buettner, Florian .

BIOINFORMATICS, 2016, 32 (08) :1241-1243

[2]

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development [J].

Bendall, Sean C. ;

Davis, Kara L. ;

Amir, El-ad David ;

Tadmor, Michelle D. ;

Simonds, Erin F. ;

Chen, Tiffany J. ;

Shenfeld, Daniel K. ;

Nolan, Garry P. ;

Pe'er, Dana .

CELL, 2014, 157 (03) :714-725

[3]

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells [J].

Buettner, Florian ;

Natarajan, Kedar N. ;

Casale, F. Paolo ;

Proserpio, Valentina ;

Scialdone, Antonio ;

Theis, Fabian J. ;

Teichmann, Sarah A. ;

Marioni, John C. ;

Stegie, Oliver .

NATURE BIOTECHNOLOGY, 2015, 33 (02) :155-160

[4]

Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps [J].

Coifman, RR ;

Lafon, S ;

Lee, AB ;

Maggioni, M ;

Nadler, B ;

Warner, F ;

Zucker, SW .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (21) :7426-7431

[5]

Origin of blood cells and HSC production in the embryo [J].

Costa, Guilherme ;

Kouskoff, Valerie ;

Lacaud, Georges .

TRENDS IN IMMUNOLOGY, 2012, 33 (05) :215-223

[6]

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data [J].

Finak, Greg ;

McDavid, Andrew ;

Yajima, Masanao ;

Deng, Jingyuan ;

Gersuk, Vivian ;

Shalek, Alex K. ;

Slichter, Chloe K. ;

Miller, Hannah W. ;

McElrath, M. Juliana ;

Prlic, Martin ;

Linsley, Peter S. ;

Gottardo, Raphael .

GENOME BIOLOGY, 2015, 16

[7]

Gut G, 2015, NAT METHODS, V12, P951, DOI [10.1038/NMETH.3545, 10.1038/nmeth.3545]

[8]

Diffusion maps for high-dimensional single-cell analysis of differentiation data [J].

Haghverdi, Laleh ;

Buettner, Florian ;

Theis, Fabian J. .

BIOINFORMATICS, 2015, 31 (18) :2989-2998

[9]

Haemangioblast commitment is initiated in the primitive streak of the mouse embryo [J].

Huber, TL ;

Kouskoff, V ;

Fehling, HJ ;

Palis, J ;

Keller, G .

NATURE, 2004, 432 (7017) :625-630

[10]

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells [J].

Klein, Allon M. ;

Mazutis, Linas ;

Akartuna, Ilke ;

Tallapragada, Naren ;

Veres, Adrian ;

Li, Victor ;

Peshkin, Leonid ;

Weitz, David A. ;

Kirschner, Marc W. .

CELL, 2015, 161 (05) :1187-1201

← 1 2 →