Alc-NTC Add2* B2m* Cfi Cp* Fbxo2 Gch1 Gfi1b Nppb Pitpnm1 Ppgb Tacr2 ALC-NTO Acbd5 B2m* Fbxo2 Frmd3 Gypa* Mlr1 Ogn Pdcd4 Sqstm1 Aldh1b1 NM_013458 NM_009735 NM_007686 NM_007752 NM_176848 NM_008102 NM_008114 NM_008726 NM_008851 NM_008906 NM_009314 NM_028793 NM_009735 NM_176848 NM_172869 NM_010369 BB298201 NM_008760 BG230003 NM_011018 NM_028270 0.0196 0.0446 0.0494 0.0225 0.0290 0.0017 0.0007 0.0103 0.0272 0.0044 0.0108 0.0292 0.0446 0.0290 0.0004 0.00001 0.0295 0.0363 0.0468 0.0357 0.0048 Off = present in ≥ 75% of arrays in control and in no arrays of alcohol-treated samples. On = not present in any control, present in ≥ 75% of arrays from alcohol-treated. Only named genes are shown. * = hematopoiesis gene. P-value: as compared with Control. Table 4 GSEA for Early Developmental Biology GO sets Comparison Keyword Gene Set Gene Set Description Size p-value Exp. 2 Control vs ALC-NTO/ ALC-NTC (see legends) Growth, Growth Regulation* GO:0016049 ^Cell growth GO:0040007 ^Growth GO:0001558 Regulation of cell GO:0040008 growth Regulation of growth GO:0005520 Insulin-like growth factor binding GO:0001525 Angiogenesis GO:0001654 Eye Development GO:0006334 Nucleosome modeling GO:0007173 Epidermal growth factor receptor (EGFR) signaling pathway ALC-NTO vs ALC-NTC Heart* Eye# Epigenetic factor~,^ Growth, Growth retardation Zhou et al. BMC Genomics 2011, 12:124 http://www.biomedcentral.com/1471-2164/12/124 Page 8 of 17 Table 3 Genes in Experiment 2 that are turned on or off by alcohol treatment Gene Symbol Genbank p-value Change in Alcohol-treated Description Off Off Off Off Off Off Off Off Off Off Off Off Off Off Off Off Off Off Off Off On 47 75 39 56 14 53 26 30 5 0.002 0.005 0.002 0.016 0.000 0.022 0.040 0.021 0.019 Adducin 2 (beta) Beta-2 microglobulin Ceruloplasmin F-box only protein 2 GTP cyclohydrolase 1 Complement component factor i Growth factor independent 1B Natriuretic peptide precursor type B Phosphatidylinositol membrane-associated 1 Protective protein for beta-Galactosidase Tachykinin receptor 2 Acyl-Coenzyme A binding domain containing 5 Beta-2 microglobulin F-box only protein 2 FERM domain containing 3 Glycophorin A Mblk1-related protein-1 Osteoglycin Programmed cell death 4 Sequestosome 1 Aldehyde dehydrogenase 1 family, member B1 Significant Genes p-value Exp. 1 (Ctgf, Igfbp2, Emp1, Osm, Cyr61, Gap43, Crim1, 0.010 Tgfb3, Igfbp7, Nov, Emp3), Gpc3, Csf1, Socs2, 0.010 Bmp6, Bmp4, Inhbb, Lepre1, Wrn, Wig1, Cish (Ctgf, Igfbp2, Osm, Cyr61, Gap43, Crim1, Igfbp7, 0.006 Nov), Gpc3, Csf1, Socs2, 0.017 Ctgf, Igfbp2, Cyr61, Crim1, Igfbp7, Nov Ctgf, Anxa2, Cyr61, Thbs1, Vegfa, Tie1, Elk3, Flt1, Crhr2, Vegfc, Kdr, Bmp4, Adra2b, Tnfrsf12a Mab21l1, Neurod1, Neurod4, Ntrk2, Fkbp8, Bmpr1b, Crb1, Stat3, Tspan5, Pax6, Bmp4, Map3k1 Hist3h2b, a; Hist1h3f; Hist1h1c; Hist1h2b, c; Hist1h3a; H1f0; Smarca2; Nap1l3 Pde6g, Egfr, Hbegf (Enriched in ALC-NTC) 0.012 0.022 0.004 0.033 0.023 ^= Gene set reduced in ALC-NTO as compared with Control. *= Gene sets reduced in ALC (all alcohol group) and ALC-NTC as compared with Control. ~= Gene set reduced in ALC as compared with Control. #= Gene set reduced in ALC-NTC as compared with Control. ( ) = genes in Cell growth related GO set, which is included in Growth GO set; or genes in Regulation of Cell growth related GO set, which is included in Regulation of Growth GO set.