Differential and correlation analyses of microarray gene expression data in the CEPH Utah families - PubMed (original) (raw)

Differential and correlation analyses of microarray gene expression data in the CEPH Utah families

Qihua Tan et al. Genomics. 2008 Aug.

Abstract

The widespread microarray technology capable of analyzing global gene expression at the level of transcription is expanding its application not only in medicine but also in studies on basic biology. This paper presents our analysis on microarray gene expression data in the CEPH Utah families focusing on the demographic characteristics such as age and sex on differential gene expression patterns. Our results show that the differential gene expression pattern between age groups is dominated by down-regulated transcriptional activities in the old subjects. Functional analysis on age-regulated genes identifies cell-cell signaling as an important functional category implicated in human aging. Sex-dependent gene expression is characterized by genes that may escape X-inactivation and, most interestingly, such a pattern is not affected by the aging process. Analysis on sibship correlation on gene expression revealed a large number of significant genes suggesting the importance of a genetic mechanism in regulating transcriptional activities. In addition, we observe an interesting pattern of sibship correlation on gene expression that increases exponentially with the mean of gene expression reflecting the enhanced genetic control over the functionally active genes.

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Figures

Figure 1

Figure 1

Heatmap with clustering of the 200 topmost significant genes displaying age-dependent expression patterns. Nearly all subjects in the two groups are clearly distinguished with the grandparents clustered to the left and grandchildren to the right panels.

Figure 2

Figure 2

Absolute z statistics plotted against the male to female ratio of mean gene expression for each of the 397 genes on the X-chromosome in the young and the old groups with the names of significant genes (FDR<0.05) marked red (19 genes in the young and 15 genes in the old groups).

Figure 3

Figure 3

Heatmap for the top 19 X-linked genes differentially expressed by sex in the young group. Among the 110 individuals, nearly all males are clustered to the left and females to the right panels.

Figure 4

Figure 4

Location of the 19 sex regulated significant genes (marked as red circles) on the X-chromosome in the young group (pseudoautosomal genes marked blue). There is an obvious concentration on the short arm (Xp) especially to the extreme end of Xp.

Figure 5

Figure 5

Scatter plot for the estimated ICC against the calculated CV (left panel) and the mean of gene expression (in log scale) (right panel) with significant genes marked in purple and insignificant genes in green.

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