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In the TGR-1 cells, 430 of 989 rapamycin modulated genes were in the set of c-Myc targets, far exceeding the expected 192 genes (P<0.000001).
When these significantly modulated genes were analyzed, according to the biological process, we could not identify any enriched GO terms for those genes whose expressions were down-regulated over time.
Tentatively, 240 and 60 modulated genes were identified as unique to EE or TAM, respectively.
Over 50% of the significantly modulated genes were present in networks.
In addition, 12 significantly modulated genes were involved in cell death and apoptosis (Table 6).
In order to compare functional annotation, protein sequences of significantly modulated genes were BLASTED against the NCBI RefSeq database [ 54].
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These results demonstrated that the spike-based normalization is interchangeable with global normalization algorithms under condition in which the representation of modulated and not modulated genes is symmetric such as that shown in Figure 8A.
In addition to these changes, an assortment of transcriptionally modulated genes was observed, which would function to maintain the level of constituents for the PG-pentapeptide precursor.
In the TDI primary chondrocyte cultures, several differently modulated genes are involved in adhesion and cytoskeleton dynamics and regulate or act along the Rac1 and CDC42 RhoGTPase signaling pathways.
The analysis of differentially modulated genes was performed using BRB-ArrayTools Version 4.3.1 developed by Dr. Richard Simon and the BRB-ArrayTools Development Team.
We found that several rexinoid-modulated genes were modulated in the mammary glands from bexarotene-treated mice.
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