cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

被引：239

作者：

Gonzalez-Blas, Carmen Bravo ^{[1
,2
]}

Minnoye, Liesbeth ^{[1
,2
]}

Papasokrati, Dafni ^{[1
,2
]}

Aibar, Sara ^{[1
,2
]}

Hulselmans, Gert ^{[1
,2
]}

Christiaens, Valerie ^{[1
,2
]}

Davie, Kristofer ^{[1
,2
]}

Wouters, Jasper ^{[1
,2
]}

Aerts, Stein ^{[1
,2
]}

机构：

[1] VIB Ctr Brain & Dis Res, Leuven, Belgium

[2] Katholieke Univ Leuven, Dept Human Genet, Leuven, Belgium

来源：

NATURE METHODS | 2019年 / 16卷 / 05期

关键词：

CHROMATIN ACCESSIBILITY; PACKAGE; INFERENCE; CLUSTERS; ELEMENTS; TOUCAN; MOUSE;

D O I：

10.1038/s41592-019-0367-1

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity in cell populations.

引用

页码：397 / +

页数：8

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