Progress and challenges in bioinformatics approaches for enhancer identification
Type
ArticleKAUST Department
Computational Bioscience Research Center (CBRC)Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Applied Mathematics and Computational Science Program
Date
2015-12-03Online Publication Date
2015-12-03Print Publication Date
2016-11Permanent link to this record
http://hdl.handle.net/10754/622949
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Show full item recordAbstract
Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.Citation
Kleftogiannis D, Kalnis P, Bajic VB (2015) Progress and challenges in bioinformatics approaches for enhancer identification. Briefings in Bioinformatics 17: 967–979. Available: http://dx.doi.org/10.1093/bib/bbv101.Sponsors
This study is supported by the KAUST Research Funds via AEA KAUST-Stanford Round 3 Global Collaborative Research Program and by KAUST Base Research Funds to PK and VBB.Publisher
Oxford University Press (OUP)Journal
Briefings in BioinformaticsAdditional Links
https://academic.oup.com/bib/article/2606433/Progressae974a485f413a2113503eed53cd6c53
10.1093/bib/bbv101
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