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They were consciously reminiscent of Olivier's film of Henry V, using the ingenuity of a Pollock's toy theatre, cut-out crowds of soldiers and cardboard banners.
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Network interactions were inferred using the Ingenuity Knowledge Base of pre-curated molecular and functional interactions mined from published literature.
Furthermore, using the Ingenuity analysis system, an upregulation of HLA genes and of the CD86 gene was found.
Molecular network analysis was carried out using the Ingenuity Knowledge Base, "a repository of molecular interactions, regulatory events, gene-to- phenotype associations, and chemical knowledge" (Ingenuity Systems 2009).
Signaling pathways containing, or regulated by, differentially expressed genes were identified using the Ingenuity Pathway Analysis (IPA) library of canonical pathways.
However, using the Ingenuity pathway analysis a number of features were immediately evident in the rapamycin treated cells: (a) A group of mRNAs involved in the inflammatory response were regulated, consistent with the immunosuppressive activity of rapamycin.
Pathway analysis using the Ingenuity package suggested the up-regulation of the Nrf2-mediated oxidative stress response and the Integrin-linked kinase (ILK) pathways.
Using the Ingenuity software, we obtained a list of upstream regulators, the most significant being the transcription factor IRF7.
Using the Ingenuity Pathway Analysis engine, the clustering of genes involved in oxidative stress response like the Nrf2 response genes and GPX suggests a role for an electrophile or oxidative stress in the mechanisms promoting renal injury in the ROP- Os/+ model [ 65].
Pathway enrichment analysis of 36 genes using the Ingenuity IPA tool.
To further analyze the biological significance of these alterations in gene expression, we used the Ingenuity Pathways Analysis; an example of the highest score in the analysis from arsenic-induced tumors is depicted.
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