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s). Because we used intensities from the IM sample in the numerator portion of gene expression ratio, the positively significant genes could be interpreted as up-regulated genes in IM samples.
The microarray data from quadruplet hybridizations for each sample were normalized with LOWESS and visualized by MA scatter plot (Fig. 3). The horizontal axis of Figure 3 (Mean of A) represents the signal intensity and the vertical axis (Mean of M) represents the gene expression difference. Representatives from significant genes determined by SAM were indicated with black arrow. Some non-significant genes with high M values were marked with red arrows.
Figure 4 depicts clustering visualization of our data. This figure is a pseudo-color representation of M values of 88 genes that were identified as significant in SAM analysis. The M value was color-coded according to its numeric value using Treeview software. The red color indicates up-regulated gene expression, while the green color indicates down-regulated gene expression.
Comparison by SAM revealed that 73 genes were more highly expressed at the IM site and 13 at the INTER site, showing higher expression within an estimated false discovery rate (FDR) of 0.163. These differentially expressed genes at each site were categorized based on the basis of the best available information regarding their biological functions. Among 73 highly expressed genes at the IM site, 6 were Expressed Sequence Tags (ESTs) and 14 were genes with unknown functions. The remaining 53 genes with known functions were categorized as being structural proteins (24, 45.3%) or as being related to metabolism (6, 11.3%), signal transduction (7, 13.2%), immune responsiveness action (6, 11.3%), cell cycling (4, 7.5%), gene/ protein expression (4, 7.5%), and oxidative stress (2, 3.8%). Meanwhile, among 13 genes that were up-regulated at the INTER site, 2 were ESTs and 6 were genes with unknown functions. The remaining set of 5 genes had functions relate
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