motifs represented within the genes that are commonly associated with differentiation of hESCs and also EtOH exposure. Thus, these motifs may represent potential binding sites of transcription factors that may play a role in differentiation changes that are occurring in hESCs upon exposure to EtOH. Furthermore, these motifs may be used as predictive signatures for genes affected by EtOH treatment. We used Similarity, Tree-building, and Alignment of DNA Motifs and Profiles (STAMP) motif analysis tool (Mahony and Benos, 2007) to determine what transcription factors could be involved in this process (Fig. 7) (Mahony and Benos, 2007). Most significant motifs and associated transcriptional factors that are correlated to EtOH treatment are shown (Fig. 7). Putting together individual module motif and transcription factor analysis, we found transcription factors well known in stem cell maintenance/differentiation such as the FOX, SMAD and POU family to be implicated, as well as transcription factors involved in hepatogenesis, suggesting alteration of differentiation in the hepatic lineage. Furthermore we performed a consensus analysis to examine possible involvement of these transcription factors in EtOH-induced molecular alterations in hESCs. We compared those genes altered by EtOH treatment against genes altered in hESCs treated with short hairpin RNA targeting OCT4 (shOCT4,
