2.2. Functional enrichment analysis

Pathway analysis of different patterns of gene expression was performed using the Sigora R package version 2.0.1, which identified pathway enrichment based on statistically over-represented Pathway Gene-Pair Signatures.^[11] Signalling Pathway Impact Analysis (SPIA) was used to assess the importance of enriched pathways in terms of their impact and ability to activate or inhibit a pathway.^[12]SPIA analysis was accomplished using the R Bioconductor package SPIA (version 2.18.0). Entrez IDs, log2-fold changes, and Q-values of all genes were compiled. SPIA produces a P value, which represents the significance level at which a pathway is found to be perturbed, and a false discovery rate (FDR). We ran SPIA using the recommended value of 2000 bootstrap iterations, and all parameters were set to their default values. A pathway was significant if the FDR was less than 0.1.