Fig. 3

VPA-induced expression measured with CAGE. a Overlap between VPA-induced and non-induced TSS clusters (see main text for cluster definition) and RefSeq promoter regions. Promoter regions were defined as the region starting from 1 kb upstream of the RefSeq TSS and ending at the start of the coding region. b Overlap between VPA- and non-induced TSS clusters and previously identified CAGE promoters preferentially expressed in visual or somatosensory cortex. c Distributions (box plots) of the ratio of CAGE tags mapping to the first exon in the VPA- and non-induced samples). Ratios were computed by dividing the number of CAGE tags mapping to the first exon with the number of tags mapping anywhere along the length of the whole gene (including introns) in all genes with at least 10 CAGE tags mapping to the gene. d Selected gene ontology terms for RefSeq genes overlapping tss clusters (overlap definition as in A). VPA-induced and non-induced TSS clusters were analyzed separately using GOStat [42], the full list of significant terms is listed in Additional file 4: Table S3. e Overlap between RefSeq genes overlapping TSS clusters according to the definition in A, and a list of selected VPA induced genes associated with brain development and chromatin regulation. The intersecting genes have alternative promoters that respond differentially to VPA induction. The full list of genes is listed in Additional file 3: Table S2 along with TSS clusters. f Distributions (density plots) of the distance between VPA-induced (VPA-i) and non-induced (non-i) TSS clusters and the closest DHSS