Identification of spatial expression trends in single-cell gene expression data

被引：222

作者：

Edsgard, Daniel ^{[1
,2
]}

Johnsson, Per ^{[1
,2
]}

Sandberg, Rickard ^{[1
,2
]}

机构：

[1] Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden

[2] Ludwig Inst Canc Res, Stockholm, Sweden

来源：

NATURE METHODS | 2018年 / 15卷 / 05期

基金：

欧洲研究理事会; 瑞典研究理事会;

关键词：

REVEALS;

D O I：

10.1038/nmeth.4634

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

As methods for measuring spatial gene expression at single-cell resolution become available, there is a need for computational analysis strategies. We present trendsceek, a method based on marked point processes that identifies genes with statistically significant spatial expression trends. trendsceek finds these genes in spatial transcriptomic and sequential fluorescence in situ hybridization data, and also reveals significant gene expression gradients and hot spots in low-dimensional projections of dissociated single-cell RNA-seq data.

引用

页码：339 / +

页数：7

共 23 条

[1]

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

[2]

Brennecke P, 2013, NAT METHODS, V10, P1093, DOI [10.1038/nmeth.2645, 10.1038/NMETH.2645]

[3]

Spatially resolved, highly multiplexed RNA profiling in single cells [J].

Chen, Kok Hao ;

Boettiger, Alistair N. ;

Moffitt, Jeffrey R. ;

Wang, Siyuan ;

Zhuang, Xiaowei .

SCIENCE, 2015, 348 (6233)

[4]

Cressie N., 1993, Statistics for spatial data

[5]

Diffusion pseudotime robustly reconstructs lineage branching [J].

Haghverdi, Laleh ;

Buettner, Maren ;

Wolf, F. Alexander ;

Buettner, Florian ;

Theis, Fabian J. .

NATURE METHODS, 2016, 13 (10) :845-+

[6]

KLF6-SV1 Drives Breast Cancer Metastasis and Is Associated with Poor Survival [J].

Hatami, Raheleh ;

Sieuwerts, Anieta M. ;

Izadmehr, Sudeh ;

Yao, Zhong ;

Qiao, Rui Fang ;

Papa, Luena ;

Look, Maxime P. ;

Smid, Marcel ;

Ohlssen, Jessica ;

Levine, Alice C. ;

Germain, Doris ;

Burstein, David ;

Kirschenbaum, Alexander ;

DiFeo, Analisa ;

Foekens, John A. ;

Narla, Goutham .

SCIENCE TRANSLATIONAL MEDICINE, 2013, 5 (169)

[7]

Illian J., 2008, STAT ANAL MODELLING, P363

[8]

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity [J].

Joost, Simon ;

Zeisel, Amit ;

Jacob, Tina ;

Sun, Xiaoyan ;

La Manno, Gioele ;

Lonnerberg, Peter ;

Linnarsson, Sten ;

Kasper, Maria .

CELL SYSTEMS, 2016, 3 (03) :221-+

[9]

Kharchenko PV, 2014, NAT METHODS, V11, P740, DOI [10.1038/nmeth.2967, 10.1038/NMETH.2967]

[10]

LOVE MI, 2014, GENOME BIOL, V15, DOI DOI 10.1186/S13059-014-0550-8

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