Fig. 6

Cord blood ASD DMRs are significantly enriched for motifs for fetal brain-relevant methyl-sensitive transcription factors. Sequences in ASD DMRs were analyzed for enrichment in known transcription factor binding motifs compared to background regions using the Hypergeometric Optimization of Motif EnRichment (HOMER) tool. The fold enrichment for top enriched motifs was plotted for the indicated DMR sets for a DMRs on autosomes or b DMRs on chromosome X. Motifs were ordered by replicated sex and direction and plotted on the same scale. Top enriched (white dots) motifs were identified as those with a q-value less than 0.05 and present in the top quartile of fold enrichment and −log(q-value) within that DMR set. Plotted motifs were the top enriched in both discovery and replication sets of DMRs for that sex and direction. c Expression of transcription factors with top enriched motifs in male or female fetal brain; proportion of ChIP-seq peaks in unmethylated (less than 10%), partially methylated (10–90%), and methylated (greater than 90%) contexts; and top ranked chromatin state by mean rank of odds ratio and p value for motif in male or female fetal brain and with a q-value less than 0.05. d Odds ratios for enrichment of top enriched motif locations in male or female fetal brain chromatin states. Top enriched (white dots) chromatin states were identified as those with a q-value less than 0.05 and present in the top quartile of odds ratio and −log(q-value) within that tissue (pooled males TD n = 56, ASD n = 56; pooled females TD n = 20, ASD n = 20). RPKM, reads per kilobase per million reads