Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites
Joint Authors
Wang, Guohua
Liu, Yunlong
Wang, Fang
Huang, Qian
Wang, Yadong
Li, Yu
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-09-03
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
Transcription factors are proteins that bind to DNA sequences to regulate gene transcription.
The transcription factor binding sites are short DNA sequences (5–20 bp long) specifically bound by one or more transcription factors.
The identification of transcription factor binding sites and prediction of their function continue to be challenging problems in computational biology.
In this study, by integrating the DNase I hypersensitive sites with known position weight matrices in the TRANSFAC database, the transcription factor binding sites in gene regulatory region are identified.
Based on the global gene expression patterns in cervical cancer HeLaS3 cell and HelaS3-ifnα4h cell (interferon treatment on HeLaS3 cell for 4 hours), we present a model-based computational approach to predict a set of transcription factors that potentially cause such differential gene expression.
Significantly, 6 out 10 predicted functional factors, including IRF, IRF-2, IRF-9, IRF-1 and IRF-3, ICSBP, belong to interferon regulatory factor family and upregulate the gene expression levels responding to the interferon treatment.
Another factor, ISGF-3, is also a transcriptional activator induced by interferon alpha.
Using the different transcription factor binding sites selected criteria, the prediction result of our model is consistent.
Our model demonstrated the potential to computationally identify the functional transcription factors in gene regulation.
American Psychological Association (APA)
Wang, Guohua& Wang, Fang& Huang, Qian& Li, Yu& Liu, Yunlong& Wang, Yadong. 2015. Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites. BioMed Research International،Vol. 2015, no. 2015, pp.1-7.
https://search.emarefa.net/detail/BIM-1056644
Modern Language Association (MLA)
Wang, Guohua…[et al.]. Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites. BioMed Research International No. 2015 (2015), pp.1-7.
https://search.emarefa.net/detail/BIM-1056644
American Medical Association (AMA)
Wang, Guohua& Wang, Fang& Huang, Qian& Li, Yu& Liu, Yunlong& Wang, Yadong. Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-7.
https://search.emarefa.net/detail/BIM-1056644
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1056644