Finding edging genes from microarray data

An, Jiyuan and Chen, Yi-Ping Phoebe 2008, Finding edging genes from microarray data, Journal of biotechnology, vol. 135, no. 3, pp. 233-240.

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Title Finding edging genes from microarray data
Author(s) An, Jiyuan
Chen, Yi-Ping Phoebe
Journal name Journal of biotechnology
Volume number 135
Issue number 3
Start page 233
End page 240
Publisher Elsevier BV
Place of publication Amsterdam, Netherlands
Publication date 2008-06-30
ISSN 0168-1656
1873-4863
Keyword(s) microarray data analysis; ;
edging genes
classifications
Summary Motivation: A set of genes and their gene expression levels are used to classify disease and normal tissues. Due to the massive number of genes in microarray, there are a large number of edges to divide different classes of genes in microarray space. The edging genes (EGs) can be co-regulated genes, they can also be on the same pathway or deregulated by the same non-coding genes, such as siRNA or miRNA. Every gene in EGs is vital for identifying a tissue's class. The changing in one EG's gene expression may cause a tissue alteration from normal to disease and vice versa. Finding EGs is of biological importance. In this work, we propose an algorithm to effectively find these EGs.

Result
: We tested our algorithm with five microarray datasets. The results are compared with the border-based algorithm which was used to find gene groups and subsequently divide different classes of tissues. Our algorithm finds a significantly larger amount of EGs than does the border-based algorithm. As our algorithm prunes irrelevant patterns at earlier stages, time and space complexities are much less prevalent than in the border-based algorithm.
Language eng
Field of Research 080301 Bioinformatics Software
HERDC Research category C1 Refereed article in a scholarly journal
HERDC collection year 2008
Copyright notice ©2008, Elsevier B.V.
Persistent URL http://hdl.handle.net/10536/DRO/DU:30017632

Document type: Journal Article
Collection: School of Engineering and Information Technology
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