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Ingenuity revealed that the differentially expressed genes might play a role in several cancer-relevant pathways (Table 1).
Furthermore, the pathway analysis of our RNA seq data (Ingenuity) also revealed that AhR and Nrf2 pathways are listed in top 25 (Supplementary Fig. 1).
Among these 464 upregulated and 791 downregulated genes, gene ontology (GO) and network analysis using Ingenuity software revealed that many were involved in cellular development, cancer and proliferation control (Fig. 3H).
Analyzing RIP-Chip data by Ingenuity software revealed that among these HuR-enriched mRNAs 49 mRNA species can be functionally assigned to cell death and survival (marked rows of Supplementary Table).
The analysis of the microarrays by Ingenuity software revealed that cell-to-cell signaling and interaction, inflammatory response, immune cell trafficking, cell-mediated immune response, immunological disease, and natural killer cell proliferation and development were amongst the most deregulated pathways under the "top diseases and biological functions" heading.
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A further evaluation performed with Ingenuity Pathway analysis revealed that these genes are nodes of networks and pathways that are involved in the modulation of Ca2+ homeostasis as well as in the regulation of glutamatergic transmission and synaptic plasticity.
Ingenuity Pathway analysis revealed that all the 5 genes induced by hemin in both endothelial cell types are regulated by the redox-sensitive master transcription factor NF-E2 related factor 2 (Nrf-2).
Ingenuity Pathway Analysis revealed that several signaling pathways were differentially affected by CoCl2 in LM-GFP and LM-miR18a cells.
There were 27 mitochondrial proteins that were downregulated in old mice, and ingenuity pathway analysis revealed that these proteins were largely involved in mitochondrial energetics (Fig. 2A).
Ingenuity Pathway Analysis revealed that significant alterations in gene expression occurred in a number of biological networks, and Myc plays a critical role in one of the primary networks.
