CSpace  > 应用数学研究所
Modeling gene regulation from paired expression and chromatin accessibility data
Duren, Zhana1,2,3; Chen, Xi2; Jiang, Rui3,4,5; Wang, Yong1; Wong, Wing Hung2
2017-06-20
Source PublicationPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN0027-8424
Volume114Issue:25Pages:E4914-E4923
AbstractThe rapid increase of genome-wide datasets on gene expression, chromatin states, and transcription factor (TF) binding locations offers an exciting opportunity to interpret the information encoded in genomes and epigenomes. This task can be challenging as it requires joint modeling of context-specific activation of cis-regulatory elements (REs) and the effects on transcription of associated regulatory factors. To meet this challenge, we propose a statistical approach based on paired expression and chromatin accessibility (PECA) data across diverse cellular contexts. In our approach, we model (i) the localization to REs of chromatin regulators (CRs) based on their interaction with sequence-specific TFs, (ii) the activation of REs due to CRs that are localized to them, and (iii) the effect of TFs bound to activated REs on the transcription of target genes (TGs). The transcriptional regulatory network inferred by PECA provides a detailed view of how trans-and cis-regulatory elements work together to affect gene expression in a context-specific manner. We illustrate the feasibility of this approach by analyzing paired expression and accessibility data from the mouse Encyclopedia of DNA Elements (ENCODE) and explore various applications of the resulting model.
Keywordgene regulation transcription factor regulatory element chromatin regulator chromatin activity
DOI10.1073/pnas.1704553114
Language英语
Funding ProjectStrategic Priority Research Program of the Chinese Academy of Sciences[XDB13000000] ; NIH[R01HG007834] ; NIH[P50HG007735] ; National Natural Science Foundation of China[11422108] ; National Natural Science Foundation of China[61671444] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[61573207]
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000403687300006
PublisherNATL ACAD SCIENCES
Citation statistics
Cited Times:30[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/25846
Collection应用数学研究所
Affiliation1.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China
2.Stanford Univ, Dept Stat, BioX Program, Dept Biomed Data Sci, Stanford, CA 94305 USA
3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
4.Tsinghua Univ, Minist Educ, Key Lab Bioinformat, Bioinformat Div, Beijing 100084, Peoples R China
5.Tsinghua Univ, Ctr Synthet & Syst Biol, Tsinghua Natl Lab Informat Sci & Technol, Dept Automat, Beijing 100084, Peoples R China
Recommended Citation
GB/T 7714
Duren, Zhana,Chen, Xi,Jiang, Rui,et al. Modeling gene regulation from paired expression and chromatin accessibility data[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2017,114(25):E4914-E4923.
APA Duren, Zhana,Chen, Xi,Jiang, Rui,Wang, Yong,&Wong, Wing Hung.(2017).Modeling gene regulation from paired expression and chromatin accessibility data.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,114(25),E4914-E4923.
MLA Duren, Zhana,et al."Modeling gene regulation from paired expression and chromatin accessibility data".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114.25(2017):E4914-E4923.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Duren, Zhana]'s Articles
[Chen, Xi]'s Articles
[Jiang, Rui]'s Articles
Baidu academic
Similar articles in Baidu academic
[Duren, Zhana]'s Articles
[Chen, Xi]'s Articles
[Jiang, Rui]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Duren, Zhana]'s Articles
[Chen, Xi]'s Articles
[Jiang, Rui]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.