This study presents a novel approach to identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray data, using the MotifModeler informatics program. The researchers developed a model to predict the most influential cis-acting elements and estimate their effects on gene expression levels under specific biological conditions. The model was applied to microarray data from a fetal alcohol syndrome (FAS) model, focusing on the 5'-regulatory region and 3'-untranslated region (3'-UTR). The results showed strong inhibitory effects of 5' cis-acting elements and stimulatory effects of 3'-UTR under alcohol treatment. This study provides a key hypothesis for the first time, suggesting that disturbances in miRNA functions may contribute to alcohol-induced developmental deficiencies in mouse embryos. The findings highlight the importance of integrating both TF and miRNA binding sites in understanding gene expression changes associated with FAS.This study presents a novel approach to identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray data, using the MotifModeler informatics program. The researchers developed a model to predict the most influential cis-acting elements and estimate their effects on gene expression levels under specific biological conditions. The model was applied to microarray data from a fetal alcohol syndrome (FAS) model, focusing on the 5'-regulatory region and 3'-untranslated region (3'-UTR). The results showed strong inhibitory effects of 5' cis-acting elements and stimulatory effects of 3'-UTR under alcohol treatment. This study provides a key hypothesis for the first time, suggesting that disturbances in miRNA functions may contribute to alcohol-induced developmental deficiencies in mouse embryos. The findings highlight the importance of integrating both TF and miRNA binding sites in understanding gene expression changes associated with FAS.