GSEA analysis using the GO biological function categories selected as being related to development (Additional files 1 and 2.) identified 20 enriched sets in Experiment 2. Of these 20 sets, 9 were also identified by Experiment 1 (Table 4). Included in these shared gene sets are multiple GO categories related to growth, eye and heart development, and epigenetics. When comparing the control embryos to all alcohol treated embryos, there were 7 GO categories that were enriched in the control groups (i.e., down-regulated in the alcohol-treated groups): five growth-related GO sets, one epigenetics (histone and chromatin regulator) GO set, and one angiogenesis GO set (Table 4). No gene set was enriched in the alcohol-treated group. An example of gene enrichment analysis is shown in Figure 4 for GO:0040007, Growth. This gene set contained 75 genes. The GSEA p-values for this enrichment score were 0.010 in Experiment 1 and 0.005 in Experiment 2.
