Biological pathway analysis

Existing microarray data from our laboratory was analyzed for pathways that were significantly altered following 1 nM E2 treatment for five days using the Ingenuity Pathway Analysis software (IPA, Ingenuity Systems, Inc., Redwood City, CA; http://www.ingenuity.com). Significant canonical pathways in which the Differentially Expressed Genes (DEGs) in the tested samples were enriched were identified. The IPA program applies Fisher’s exact test to calculate a p-value that represents the probability of the DEGs in the pathway being found together due to random chance. Specifically, genes identified in the microarray with differential expression p-values ≤0.05 and fold-changes ≥1.5 were used as focus genes. Pathways with p-values < 0.05 were significantly enriched.