The NOD-like receptor signaling pathway. These analyses again suggest that the

The NOD-like receptor signaling pathway. These analyses again suggest that the immune and DMXB-A chemical information inflammatory responses are common cochlear responses to acoustic overstimulation in both species. 3.4. Identification of the common upstream regulators of the differentially expressed genes IPA was used to determine the upstream transcriptional regulators of the differentially expressed genes. This bioinformatics tool identifies the genes, molecules and chemicals that regulate the transcription of genes of interest. The activation states of transcriptional regulators can be predicted based on the observed differential regulation of the genes in a dataset. To reduce the identification of false positives, we used a stringent bias-corrected zscore > 2 for activation and < -2 for inhibition. We identified 45 upstream regulators in the rat samples and 20 in the mouse samples that were predicted to activate the expression of the differentially expressed genes. Of those upstream regulators, 10 were identified in both species, and of these 10 common regulators, eight have roles in the immune response and six are cytokines. This observation suggests that the common regulators of the differentially expressed genes are molecules related to the immune response. We also identified 18 regulators in the rat and six in the mouse that were predicted to inhibit the expression of the differentially expressed genes. Among those, three were identified in both species. Tp73 and Nkx2-3 are transcription factors, and MAPK1 is an extracellular signal-regulated kinase that has been implicated in acoustic trauma to the cochlea. 3.5. Common cellular components To analyze the cellular distribution, we identified three terms for the mouse and five terms for the rat that showed an FDR < 0.05. All three terms that were identified in the mouse samples were related to the extracellular space. These terms were also identified in the rat samples, and their FDR values were the lowest among the terms identified in the rat. The two additional terms that were identified in the rat but not in the mouse were related to the plasma membrane and the cell surface, and those two terms were also functionally related to the extracellular space. Together, this analysis suggests that the differentially expressed genes have a strong link PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19854301 to the extracellular space. 3.6. Comparison of the differentially expressed genes between the rat and mouse samples Given the similarity in the biological functions and the molecular pathways in the mouse and rat cochleae, we sought to determine the common differentially expressed genes that were shared by the two species. A total of 31 genes were identified, among which 29 were upregulated and two were downregulated. All of the overlapping genes displayed the same direction of SB366791 supplier change, i.e., the genes that were upregulated in one species were also upregulated in the other, and vice versa. A large portion of the differentially expressed genes did not overlap between the mouse and rat samples. One reason for this discrepancy is that some genes identified in one species do not have orthologues in the other species. To determine the extent to which this factor contributed, we determined the number of differentially expressed genes identified in one species that did not have an orthologue in the other species. A total of 14 of the 101 differentially expressed genes in the mouse do not have the homologs in the rat, and among the 555 differentially expressed genes identifi.The NOD-like receptor signaling pathway. These analyses again suggest that the immune and inflammatory responses are common cochlear responses to acoustic overstimulation in both species. 3.4. Identification of the common upstream regulators of the differentially expressed genes IPA was used to determine the upstream transcriptional regulators of the differentially expressed genes. This bioinformatics tool identifies the genes, molecules and chemicals that regulate the transcription of genes of interest. The activation states of transcriptional regulators can be predicted based on the observed differential regulation of the genes in a dataset. To reduce the identification of false positives, we used a stringent bias-corrected zscore > 2 for activation and < -2 for inhibition. We identified 45 upstream regulators in the rat samples and 20 in the mouse samples that were predicted to activate the expression of the differentially expressed genes. Of those upstream regulators, 10 were identified in both species, and of these 10 common regulators, eight have roles in the immune response and six are cytokines. This observation suggests that the common regulators of the differentially expressed genes are molecules related to the immune response. We also identified 18 regulators in the rat and six in the mouse that were predicted to inhibit the expression of the differentially expressed genes. Among those, three were identified in both species. Tp73 and Nkx2-3 are transcription factors, and MAPK1 is an extracellular signal-regulated kinase that has been implicated in acoustic trauma to the cochlea. 3.5. Common cellular components To analyze the cellular distribution, we identified three terms for the mouse and five terms for the rat that showed an FDR < 0.05. All three terms that were identified in the mouse samples were related to the extracellular space. These terms were also identified in the rat samples, and their FDR values were the lowest among the terms identified in the rat. The two additional terms that were identified in the rat but not in the mouse were related to the plasma membrane and the cell surface, and those two terms were also functionally related to the extracellular space. Together, this analysis suggests that the differentially expressed genes have a strong link PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19854301 to the extracellular space. 3.6. Comparison of the differentially expressed genes between the rat and mouse samples Given the similarity in the biological functions and the molecular pathways in the mouse and rat cochleae, we sought to determine the common differentially expressed genes that were shared by the two species. A total of 31 genes were identified, among which 29 were upregulated and two were downregulated. All of the overlapping genes displayed the same direction of change, i.e., the genes that were upregulated in one species were also upregulated in the other, and vice versa. A large portion of the differentially expressed genes did not overlap between the mouse and rat samples. One reason for this discrepancy is that some genes identified in one species do not have orthologues in the other species. To determine the extent to which this factor contributed, we determined the number of differentially expressed genes identified in one species that did not have an orthologue in the other species. A total of 14 of the 101 differentially expressed genes in the mouse do not have the homologs in the rat, and among the 555 differentially expressed genes identifi.