We derived a proliferation signature from in vitro microarray studies based only on genes that differ in expression in different parts of the cell cycle (Whitfield et al, 2002; Chang et al, 2004).
When we determined how many genes differ in expression level across different regions of the brain by ≥2 quintiles in ≥2 regions of the brain, only 30 (∼10%) of the genes qualify as showing variability in expression level across different regions of the brain (Table 1).
As a mechanism for local sensitivities to systemic levels of 20E, we hypothesized that groups of cells that responded differently to 20E manipulations would differ in expression of ecdysone receptor (EcR).
The picture that is emerging from the animal studies discussed above is that a relatively small group of proteins differ in expression between oocytes in different quality or maturation groups.
Notably, genes whose expression change in different directions in 3BKO-BL31 and -LCLs also differ in expression between naïve B-cells and centroblasts.
For example, between the cerebellum and cortex only 75 of the 270 genes show differences of any magnitude and of these only 6 differ in expression by values that would seem to be significant (greater than 2 quintiles in level).
We then compared these genes affected by human and chimpanzee diet differences in mouse to the 1,169 orthologous genes that differ in expression when human and chimpanzee livers are compared [13].
In this context, homologous genes that differ in expression characteristics despite the absence of any meaningful differences in upstream regulatory sequence architecture should justify examination of the contribution of differential upstream DNA methylation in the expression of the desired phenotype (Figure 3B).
Interestingly, miRNAs with expression differences between tissues show often tissue-specific patterns, that is, these miRNAs differ in expression in only one tissue while expression is unchanged in the other four tissues.
These molecules differ in expression level, location, pathological stimulation, and/or endocytic pathway.
This method allowed for the identification of proteins that differ in expression levels in liver tissue or in plasma with disease progression from liver fibrosis, cirrhosis or steatohepatitis to HCC.
