Efficient Identification of Transcription Factor Binding Sites with a Graph Theoretic Approach
Joint Authors
Source
Computational and Mathematical Methods in Medicine
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-6, 6 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-01-03
Country of Publication
Egypt
No. of Pages
6
Main Subjects
Abstract EN
Identifying transcription factor binding sites with experimental methods is often expensive and time consuming.
Although many computational approaches and tools have been developed for this problem, the prediction accuracy is not satisfactory.
In this paper, we develop a new computational approach that can model the relationships among all short sequence segments in the promoter regions with a graph theoretic model.
Based on this model, finding the locations of transcription factor binding site is reduced to computing maximum weighted cliques in a graph with weighted edges.
We have implemented this approach and used it to predict the binding sites in two organisms, Caenorhabditis elegans and mus musculus.
We compared the prediction accuracy with that of the Gibbs Motif Sampler.
We found that the accuracy of our approach is higher than or comparable with that of the Gibbs Motif Sampler for most of tested data and can accurately identify binding sites in cases where the Gibbs Motif Sampler has difficulty to predict their locations.
American Psychological Association (APA)
Song, Jia& Xu, Li& Sun, Hong. 2013. Efficient Identification of Transcription Factor Binding Sites with a Graph Theoretic Approach. Computational and Mathematical Methods in Medicine،Vol. 2013, no. 2013, pp.1-6.
https://search.emarefa.net/detail/BIM-503719
Modern Language Association (MLA)
Song, Jia…[et al.]. Efficient Identification of Transcription Factor Binding Sites with a Graph Theoretic Approach. Computational and Mathematical Methods in Medicine No. 2013 (2013), pp.1-6.
https://search.emarefa.net/detail/BIM-503719
American Medical Association (AMA)
Song, Jia& Xu, Li& Sun, Hong. Efficient Identification of Transcription Factor Binding Sites with a Graph Theoretic Approach. Computational and Mathematical Methods in Medicine. 2013. Vol. 2013, no. 2013, pp.1-6.
https://search.emarefa.net/detail/BIM-503719
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-503719