GO and pathway analysis

Gene ontology (GO) analysis (www.geneontology.org) was used to investigate biological functions based on differentially expressed coding genes [15]. This analysis classifies functions according to the three following aspects: biological process, cellular component and molecular function. Fisher’s exact test was applied to classify the GO category. The P-value denotes the significance of GO term enrichment in the deregulated expressed genes. A lower P-value indicated a higher significance of the GO term (P-value < 0.05).

Pathway analysis was applied to assess the differentially expressed coding genes according to the Kyoto Encyclopedia of Genes and Genomes (KEGG), BioCarta, and Reactome (http://www.genome.jp/kegg/) [16]. The P-value (EASE-score, Fisher-P-value or Hypergeometric-P-value) indicates the significance of the pathway correlated with the conditions. P < 0.05 was considered statistically significant.