Computational and Systems Biology Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.
Nucleic Acids Res. 2022 May 20;50(9):e52. doi: 10.1093/nar/gkac036.
Genomic interactions provide important context to our understanding of the state of the genome. One question is whether specific transcription factor interactions give rise to genome organization. We introduce spatzie, an R package and a website that implements statistical tests for significant transcription factor motif cooperativity between enhancer-promoter interactions. We conducted controlled experiments under realistic simulated data from ChIP-seq to confirm spatzie is capable of discovering co-enriched motif interactions even in noisy conditions. We then use spatzie to investigate cell type specific transcription factor cooperativity within recent human ChIA-PET enhancer-promoter interaction data. The method is available online at https://spatzie.mit.edu.
基因组相互作用为我们理解基因组的状态提供了重要的背景信息。一个问题是，特定的转录因子相互作用是否会导致基因组组织。我们引入了 spatzie，这是一个 R 包和一个网站，它实现了增强子-启动子相互作用中显著转录因子基序协同作用的统计测试。我们在来自 ChIP-seq 的真实模拟数据下进行了对照实验，以确认 spatzie 能够发现即使在嘈杂条件下也能协同富集的基序相互作用。然后，我们使用 spatzie 研究了最近的人类 ChIA-PET 增强子-启动子相互作用数据中细胞类型特异性转录因子协同作用。该方法可在 https://spatzie.mit.edu 在线获得。
Zotero 插件
