Nonlinear Model-Based Method for Clustering Periodically Expressed Genes
Joint Authors
Tian, Li-Ping
Liu, Li-Zhi
Zhang, Qian-Wei
Wu, Fang-Xiang
Source
Issue
Vol. 2011, Issue 2011 (31 Dec. 2011), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2011-11-01
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Medicine
Information Technology and Computer Science
Abstract EN
Clustering periodically expressed genes from their time-course expression data could help understand the molecular mechanism of those biological processes.
In this paper, we propose a nonlinear model-based clustering method for periodically expressed gene profiles.
As periodically expressed genes are associated with periodic biological processes, the proposed method naturally assumes that a periodically expressed gene dataset is generated by a number of periodical processes.
Each periodical process is modelled by a linear combination of trigonometric sine and cosine functions in time plus a Gaussian noise term.
A two stage method is proposed to estimate the model parameter, and a relocation-iteration algorithm is employed to assign each gene to an appropriate cluster.
A bootstrapping method and an average adjusted Rand index (AARI) are employed to measure the quality of clustering.
One synthetic dataset and two biological datasets were employed to evaluate the performance of the proposed method.
The results show that our method allows the better quality clustering than other clustering methods (e.g., k-means) for periodically expressed gene data, and thus it is an effective cluster analysis method for periodically expressed gene data.
American Psychological Association (APA)
Tian, Li-Ping& Liu, Li-Zhi& Zhang, Qian-Wei& Wu, Fang-Xiang. 2011. Nonlinear Model-Based Method for Clustering Periodically Expressed Genes. The Scientific World Journal،Vol. 2011, no. 2011, pp.1-11.
https://search.emarefa.net/detail/BIM-1027879
Modern Language Association (MLA)
Tian, Li-Ping…[et al.]. Nonlinear Model-Based Method for Clustering Periodically Expressed Genes. The Scientific World Journal No. 2011 (2011), pp.1-11.
https://search.emarefa.net/detail/BIM-1027879
American Medical Association (AMA)
Tian, Li-Ping& Liu, Li-Zhi& Zhang, Qian-Wei& Wu, Fang-Xiang. Nonlinear Model-Based Method for Clustering Periodically Expressed Genes. The Scientific World Journal. 2011. Vol. 2011, no. 2011, pp.1-11.
https://search.emarefa.net/detail/BIM-1027879
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1027879