Zhou et al. BMC Genomics 2011, 12:124 http://www.biomedcentral.com/1471-2164/12/124 Page 5 of 17 Figure 2 The red blood vessels were less distinguishable in the yolk sac (arrow, left) and embryo (arrow, right) in the alcohol-treated group as compared with those of the Control. All embryos examined for red blood vessels had active heart beat at the termination of experiment. Figure 3 Hierarchical clustering by arrays in Experiment 1 and Experiment 2. 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 enrich- ment 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 Experi- ment 1 and 0.005 in Experiment 2. The growth-related genes represented the largest group of affected genes. There were 5 GO sets of growth- associated genes (Table 4). Many of these genes, identi- fied by GSEA in both experiments, were also identified in Experiment 2 at the single gene level; e.g. the Growth gene set (GO:0040007): Ctgf, Igfbp2, Emp1, Osm, Cyr61, Gap43, Crim1, Tgfb3, Nov, Socs2, and Wrn were signifi- cantly reduced in Experiment 2, and Igfbp7, Emp3, Bmp4, Bmp6, Inhbb, Wig1, and Cish were reduced but