Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data
文献类型：期刊论文
| 作者 | Zamanighomi, Mahdi1; Lin, Zhixiang1; Wang, Yong2 ; Jiang, Rui3,4; Wong, Wing Hung1,5
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| 刊名 | NUCLEIC ACIDS RESEARCH
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| 出版日期 | 2017-06-02 |
| 卷号 | 45期号:10页码:5666-5677 |
| ISSN号 | 0305-1048 |
| DOI | 10.1093/nar/gkx358 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000402510700021 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/25639]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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