The significance of the association between the data set and the canonical pathway was measured in two ways: a) a ratio of the number of molecules from the data set that map to the pathway divided by the total number of molecules that map to the canonical pathway is displayed. b) Fisher’s exact test was used to calculate a p-value determining the probability that the association between the genes in the dataset and the canonical pathway is explained by chance alone. Hierarchical clustering analysis with normalized data shows that batch effects are clearly evident in all studies even after normalization. Arrays that were hybridized on the same date as a batch are clustered together in the dendrogram. We used an Empirical Bayes method implemented in ComBat to remove batch effects. Batch effects were completely removed from the BL, B7, and K9 data and considerably removed from the B7 and B8 data. Data were integrated between the rgu34a chip which had a total of 8799 probe-sets and rae230a chip that had a total of 15923 probe-sets. After data integration, the rg_exclu category contained 2356 probe-sets exclusive to the rgu34a array only. The all5_com category included 6384 rgu34a unique probe-sets mapping to 5435 rae230a unique probe-sets that are common among all five studies. Finally, the rae_exclu category contained 10,431 probesets exclusive to the rae230a array type. The results show that formation of cells, quantity and synthesis of inositol phosphate, and axonogenesis. Thus they affect the cell death and survival, cellular growth and proliferation, carbohydrate metabolism, molecular transport, small molecule biochemistry, cell morphology, and nervous system development and function in the aged animals. Major functions categories that see an increase are cellular movement, cellular development, and connective tissue development and function. The specific functions of the genes in this category include the migration of cells and differentiation of chondrocytes. We have generated biological knowledge based gene interaction networks for the AY 4-(Benzyloxy)phenol significant genes. A representative network graph is presented in Figure 6, which shows the network interactions of some of the aging and learning genes. A summary of the functions for the top five most significant networks is given in Table 4. The most critical canonical pathways that are affected in the aged animals include Eif2 signaling, antigen presentation, and Ox40 signaling pathways. A total of 738 genes with significant effect sizes were used as input for the IU functional analysis in the IPA. Though cell viability of hippocampal neurons and CNS cells, cellto-cell signaling, and molecular transport were the top functions in the results, none were statistically significant. However, when we reanalyzed with an effect size data set that was generated comparing the expression level of the aged-impaired animals with that of the aged-unimpaired animals without any controls, four functions e.g. molecular transport, cellular development, cellular growth and proliferation, and connective tissue development and function were significantly decreased. The specific functions of these genes in these categories include transport of molecules and proliferation of fibroblast cell lines. In Epimedoside-A addition, growth of neuritis was also decreased among others. Similar to AY, we have generated biological knowledge based gene interaction networks for the IU related genes. A summary of the functions for the top five most significant networks is given in Table 7.