Discovery of deep order-preserving submatrix in DNA microarray data based on sequential pattern mining
by Zhiwen Liu; Yun Xue; Meihang Li; Bo Ma; Meizhen Zhang; Xin Chen; Xiaohui Hu
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 17, No. 3, 2017

Abstract: In recent years, order-preserving submatrix (OPSM) model has been widely used in gene expression data analysis. Since it focuses on the changes between the elements rather than the real value, it shows better robustness and statistical significance among results than other models do. Currently, many OPSM algorithms are heuristic. They cannot mine all OPSMs as well as the deep OPSMs which are of biological significance in gene expression data. In this paper, an exact algorithm is proposed to find OPSMs by using frequent sequential pattern mining method. Firstly, we find out all common subsequences (ACS) between any two rows through dynamic programming. Then, we store them into a suffix tree. After that, we can get all OPSMs in this suffix tree, including deep OPSMs. Verified by the real gene data and artificially synthesised data, it is proved that our algorithm is efficient and meaningful.

Online publication date: Wed, 19-Jul-2017

The full text of this article is only available to individual subscribers or to users at subscribing institutions.

 
Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.

Pay per view:
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.

Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Data Mining and Bioinformatics (IJDMB):
Login with your Inderscience username and password:

    Username:        Password:         

Forgotten your password?


Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.

If you still need assistance, please email subs@inderscience.com