Direct binding of RAR mediates the initial response to RA during early neurogenesis. Genes with more than five-fold differential expression after 8 hours of RA exposure are listed. RAR binds to many of the up-regulated genes, with binding more likely for greater degrees of up-regulation. Red arrows indicate post-RA RAR binding within 20 kbp of the gene. Black dashed lines indicate pre-RA RAR binding within 20 kbp. Three functional groups of genes are indicated by coloring the gene names. Information for all more than two-fold differentially expressed genes is tabulated in Additional file 2.