294 Current Genomics, 2010, Vol. 11, No. 4 Yu et al. Fig. (8). Heat map for genes pertaining to apoptotic nuclear changes (GO: 0030262). Columns represent microarray data ob- tained from independent cultures of cells of the indicated genotype and therefore represent biological replicates. Gene name abbrevia- tions for each component of the gene set are indicated at the end of each row. Green indicates expression is lower, while red indicates expression is higher than average of WT. The genes in this set are predominantly upregulated in the transgenic cells (TgS1/2/3/4/5/6/ 7) in the presence of serum relative to the WT cells treated with serum (WTS1/2/3/4/5/6/7). have been limited (reviewed in [23]). No specific molecular signature for hypertrophy has been described, as transcrip- tional profiles are divergent in different models of hypertro- phy [29]. The advantage of Gene Set Analysis and its rela- tive, Gene Set Enrichment Analysis, is that it more readily detects small concordant changes in the expression of genes acting in concert, which may alter the flux through a path- way more readily than a more dramatic change in a single gene [18]. A caveat to this method is that the individual genes within a gene set may not have significantly different gene expression by single gene analysis, and therefore the relevance of gene components within each set cannot easily be validated. Nevertheless, the method is useful for generat- Fig. (9). Heat map for genes involved in mitochondrion organiza- tion and biogenesis (GO: 0007005). Columns represent microarray data obtained from independent cultures of cells of the indicated genotype and therefore represent biological replicates. Gene name abbreviations for each component of the gene set are indicated at the end of each row. Green indicates expression is lower, while red indicates expression is higher than average of WT. The genes in this set are predominantly upregulated in the transgenic cells (TgS1/2/3/4/5/6/7) in the presence of serum relative to the WT cells treated with serum (WTS1/2/3/4/5/6/7). ing hypotheses for further experimentation. Using this method, we have identified potential roles for genes involved in water transport, regulation of adenylate cyclase activity, protein dephosphorylation, embryonic development, apopto- sis and mitochondrial biogenesis, although the exact mecha- nisms by which these gene products may affect hypertrophy will require further study.