Bioinformatics
Functional interpretation of differentially expressed genes was analyzed in the context of gene ontology and molecular networks using the Ingenuity Pathways Analysis (IPA) 6.5 software (Ingenuity Systems®; http://www.ingenuity.com). The differentially expressed genes were categorized, compared to genetic categories in the IPA database, and ranked according to p-values [54]. The IPA analysis determined the subcategories within each category which is supplied with an appropriate p-value and the number of genes identified. Since the size of the created network could potentially be enormous, the IPA software limited the number of molecules in the network to 35, leaving only the most important ones based on the number of connections for each focus gene (focus genes = a subset of uploaded significant genes having direct interactions with other genes in the database) to other significant genes [55].