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. 2009 Oct;94(4):257-62.
doi: 10.1016/j.ygeno.2009.05.008. Epub 2009 May 29.

Differentially expressed genes strongly correlated with femur strength in rats

Imranul Alam  1 , Qiwei Sun, Daniel L Koller, Lixiang Liu, Yunlong Liu, Howard J Edenberg, Jiliang Li, Tatiana Foroud, Charles H Turner
Affiliations

Differentially expressed genes strongly correlated with femur strength in rats

Imranul Alam et al. Genomics. 2009 Oct.

Abstract

The region of chromosome 1q33-q54 harbors quantitative trait loci (QTL) for femur strength in COPxDA and F344xLEW F2 rats. The purpose of this study is to identify the genes within this QTL region that contribute to the variation in femur strength. Microarray analysis was performed using RNA extracted from femurs of COP, DA, F344 and LEW rats. Genes differentially expressed in the 1q33-q54 region among these rat strains were then ranked based on the strength of correlation with femur strength in F2 animals derived from these rats. A total of 214 genes in this QTL region were differentially expressed among all rat strains, and 81 genes were found to be strongly correlated (r(2)>0.50) with femur strength. Of these, 12 candidate genes were prioritized for further validation, and 8 of these genes (Ifit3, Ppp2r5b, Irf7, Mpeg1, Bloc1s2, Pycard, Sec23ip, and Hps6) were confirmed by quantitative PCR (qPCR). Ingenuity Pathway Analysis suggested that these genes were involved in interferon alpha, nuclear factor-kappa B (NFkB), extracellular signal-related kinase (ERK), hepatocyte nuclear factor 4 alpha (HNF4A) and tumor necrosis factor (TNF) pathways.

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Figures

Fig. 1
Fig. 1
Linkage analysis for femur ultimate force (Fu) for rat chromosome 1 in COP×DA and F344×LEW crosses in the region of 1q33–q54 (D1Rat52–D1Rat82). LOD scores plotted on the y axis vs. the relative microsatellite markers located along chromosome 1 on the x axis.
Fig. 2
Fig. 2
Network of the 8 candidate genes that were confirmed by qPCR (highlighted in red) for femur strength in Ingenuity Pathway Analysis (IPA). The well-known NFkB, ERK and TNF pathways related to bone metabolism is highlighted in blue.
See this image and copyright information in PMC

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