Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com) was used to assess microarray data for overrepresentation of known gene networks and biological functions. All detected genes in a data set were used as the reference set; cutoffs for fold change and the associated p value were 1.2 and 0.05, respectively. Default settings were used for all other parameters. For network analysis, network eligible molecules (data set molecules that interact with the Ingenuity Knowledge Base) were used as “seeds” to generate networks whose molecules’ interconnectedness is maximized relative to their connectedness with all molecules in the knowledge base. Network scores were calculated by taking the negative log10 of the p value computed with Fisher’s exact test. Functional analysis identified the biological functions and/or diseases that were most significant to each data set. A right-tailed Fisher’s exact test was used to calculate the p-value determining the probability that each biological function and/or disease assigned to that data set is due to chance alone.
