To assess the broad HCV relevance of our regulatory network, we used Ingenuity Pathways Analysis (IPA) to perform pathway analysis of those 1,077 mRNAs.
To reconcile differences in these different sources of regulatory network information (literature, Ingenuity, Pathway Studio), we only included an interaction in our network if it could be identified in two out of the three resources.
Pathway analysis: a relationship between genes and their connection to existing regulatory pathways was examined using Ingenuity Pathway Analysis (IPA), a web-based entry tool developed by Ingenuity Systems, Inc. (http://www.ingenuity.com ).com
To better understand how differentially expressed genes were integrated into specific regulatory and signaling pathway networks, we used Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, USA).
We searched the Ingenuity Knowledge Base for upstream regulatory molecules of the transcription factors involved in these functions and found close to 200 such regulators, of which 18 20 had significant p-values.
Changes in regulatory networks were also analysed through the use of the Ingenuity Pathways Analysis software (Ingenuity Systems, Redwood City, CA, USA).
Changes in regulatory networks were also analysed through the use of the Ingenuity Pathways Analysis software (Ingenuity® Systems, Redwood City, CA) [ 26].
In order to identify the structure of regulatory networks underlying response to wounding we performed Ingenuity Pathway Analysis (IPA).
America's shale-gas success a matter not just of helpful geology and Yankee ingenuity, but also of various legal and regulatory positions such as those of the 1978 act may prove hard to replicate in some other countries.
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).
