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A two-step strategy for detecting differential gene expression in cDNA microarray data. Curr Genet 2005 Feb;47(2):121-31

Date

02/03/2005

Pubmed ID

15688252

DOI

10.1007/s00294-004-0551-3

Scopus ID

2-s2.0-13644271264   9 Citations

Abstract

A mixed-model approach is proposed for identifying differential gene expression in cDNA microarray experiments. This approach is implemented by two interconnected steps. In the first step, we choose a subset of genes that are potentially expressed differentially among treatments with a loose criterion. In the second step, these potential genes are used for further analyses and data-mining with a stringent criterion, in which differentially expressed genes (DEGs) are confirmed and some quantities of interest (such as gene x treatment interaction) are estimated. By simulating datasets with DEGs, we compare our statistical method with a widely used method, the t-statistic, for single genes. Simulation results show that our approach produces a high power and a low false discovery rate for DEG identification. We also investigate the impacts of various source variations resulting from microarray experiments on the efficiency of DEG identification. Analysis of a published experiment studying unstable transcripts in Arabidopsis illustrates the utility of our method. Our method identifies more novel and biologically interesting unstable transcripts than those reported in the original literature.

Author List

Lu Y, Zhu J, Liu P

Author

Pengyuan Liu PhD Adjunct Professor in the Physiology department at Medical College of Wisconsin




MESH terms used to index this publication - Major topics in bold

Arabidopsis
DNA, Complementary
Gene Expression
Genes, Plant
Models, Genetic
Oligonucleotide Array Sequence Analysis
jenkins-FCD Prod-484 8aa07fc50b7f6d102f3dda2f4c7056ff84294d1d