顺式调控元件主题建模于单细胞 ATAC-seq 数据。
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.
机构信息
VIB Center for Brain & Disease Research, Leuven, Belgium.
Department of Human Genetics, KU Leuven, Leuven, Belgium.
出版信息
Nat Methods. 2019 May;16(5):397-400. doi: 10.1038/s41592-019-0367-1. Epub 2019 Apr 8.
Abstract
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.
摘要
我们提出了 cisTopic，这是一个概率框架，用于从稀疏的单细胞表观基因组学数据中同时发现共可及增强子和稳定的细胞状态（http://github.com/aertslab/cistopic）。使用来自分化造血细胞、大脑和转录因子扰动的单细胞 ATAC-seq 数据集汇编，我们证明了主题建模可用于稳健地识别细胞类型、增强子和相关转录因子。cisTopic 提供了对细胞群体中调节异质性背后机制的深入了解。
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