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Finding edging genes from microarray data

Paper ID Volume ID Publish Year Pages File Format Full-Text
25025 43553 2008 8 PDF Available
Title
Finding edging genes from microarray data
Abstract

MotivationA 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.ResultWe 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.AvailabilityThe algorithm proposed is implemented in C++ on Linux platform. The EGs in five microarray datasets are calculated. The preprocessed datasets and the discovered EGs are available at http://www3.it.deakin.edu.au/∼phoebe/microarray.html.

Keywords
Microarray data analysis; Edging genes; Classifications
First Page Preview
Finding edging genes from microarray data
Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 135, Issue 3, 30 June 2008, Pages 233–240
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering