Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data

doi:10.1093/nar/gkx358

CSpace > 应用数学研究所

	Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data
	Zamanighomi, Mahdi 1; Lin, Zhixiang 1; Wang, Yong2 ; Jiang, Rui 3,4; Wong, Wing Hung 1,5
	2017-06-02
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	45 期号:10 页码:5666-5677
摘要	Transcription factors (TFs) play crucial roles in regulating gene expression through interactions with specific DNA sequences. Recently, the sequence motif of almost 400 human TFs have been identified using high-throughput SELEX sequencing. However, there remain a large number of TFs (similar to 800) with no high-throughput-derived binding motifs. Computational methods capable of associating known motifs to such TFs will avoid tremendous experimental efforts and enable deeper understanding of transcriptional regulatory functions. We present a method to associate known motifs to TFs (MATLAB code is available in Supplementary Materials). Our method is based on a probabilistic framework that not only exploits DNA-binding domains and specificities, but also integrates open chromatin, gene expression and genomic data to accurately infer monomeric and homodimeric binding motifs. Our analysis resulted in the assignment of motifs to 200 TFs with no SELEX-derived motifs, roughly a 50% increase compared to the existing coverage.
DOI	10.1093/nar/gkx358
语种	英语
资助项目	National Institutes of Health (NIH)[R01HG007834] ; National Institutes of Health (NIH)[P50HG007735] ; NIH[R01HG007834]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000402510700021
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/25640
专题	应用数学研究所
通讯作者	Wong, Wing Hung
作者单位	1.Stanford Univ, Dept Stat, Stanford, CA 94305 USA 2.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China 3.Tsinghua Univ, TNLIST, Dept Automat, Bioinformat Div,MOE Key Lab Bioinformat, Beijing 100084, Peoples R China 4.Tsinghua Univ, Ctr Synthet & Syst Biol, Dept Automat, Beijing 100084, Peoples R China 5.Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA
推荐引用方式 GB/T 7714	Zamanighomi, Mahdi,Lin, Zhixiang,Wang, Yong,et al. Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data[J]. NUCLEIC ACIDS RESEARCH,2017,45(10):5666-5677.
APA	Zamanighomi, Mahdi,Lin, Zhixiang,Wang, Yong,Jiang, Rui,&Wong, Wing Hung.(2017).Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data.NUCLEIC ACIDS RESEARCH,45(10),5666-5677.
MLA	Zamanighomi, Mahdi,et al."Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data".NUCLEIC ACIDS RESEARCH 45.10(2017):5666-5677.