NDLI: Searching for Coexpressed Genes in Three-Color cDNA Microarray Data Using a Probabilistic Model-Based Hough Transform

Content Provider	ACM Digital Library
Author	Tiňo, gdfgdf Zhao, Hongya Yan, Hong
Abstract	The effects of a drug on the genomic scale can be assessed in a three-color cDNA microarray with the three color intensities represented through the so-called hexaMplot. In our recent study, we have shown that the Hough Transform (HT) applied to the hexaMplot can be used to detect groups of coexpressed genes in the normal-disease-drug samples. However, the standard HT is not well suited for the purpose because 1) the assayed genes need first to be hard-partitioned into equally and differentially expressed genes, with HT ignoring possible information in the former group; 2) the hexaMplot coordinates are negatively correlated and there is no direct way of expressing this in the standard HT and 3) it is not clear how to quantify the association of coexpressed genes with the line along which they cluster. We address these deficiencies by formulating a dedicated probabilistic model-based HT. The approach is demonstrated by assessing effects of the drug Rg1 on homocysteine-treated human umbilical vein endothetial cells. Compared with our previous study, we robustly detect stronger natural groupings of coexpressed genes. Moreover, the gene groups show coherent biological functions with high significance, as detected by the Gene Ontology analysis.
Starting Page	1093
Ending Page	1107
Page Count	15
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2010.120
Volume Number	8
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Three-color cDNA microarray, probabilistic Hough transform, gene coexpression, hexaMplot, gene ontology.
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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