Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice

Matthew J. Callow; Sandrine Dudoit; Elaine L. Gong; Terence P. Speed; Edward M. Rubin

doi:10.1101/gr.147200

Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice

¹Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA; ²Department of Biochemistry, Stanford University, Stanford, California 94305, USA; ³Department of Statistics and Program in Biostatistics, University of California, Berkeley, California 94720-3860, USA

Abstract

Based on the assumption that severe alterations in the expression of genes known to be involved in high-density lipoprotein (HDL) metabolism may affect the expression of other genes, we screened an array of >5000 mouse expressed sequence tags for altered gene expression in the livers of two lines of mice with dramatic decreases in HDL plasma concentrations. Labeled cDNA from livers of apolipoprotein AI (apoAI)-knockout mice, scavenger receptor BI (SR-BI) transgenic mice, and control mice were cohybridized to microarrays. Two-samplet statistics were used to identify genes with altered expression levels in the knockout or transgenic mice compared with control mice. In the SR-BI group we found nine array elements representing at least five genes that were significantly altered on the basis of an adjusted P value < 0.05. In the apoAI-knockout group, eight array elements representing four genes were altered compared with the control group (adjustedP < 0.05). Several of the genes identified in the SR-BI transgenic suggest altered sterol metabolism and oxidative processes. These studies illustrate the use of multiple-testing methods for the identification of genes with altered expression in replicated microarray experiments.