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. 2019 Jun 26;30(2):640–655. doi: 10.1093/cercor/bhz115

Figure 5.

Figure 5

Enrichment of DMR associated genes for NDD genetic risk and differentially expressed genes. (A) ASD, Dup15q, and RTT DMR associated genes significantly overlap with each other (all overlaps are FDR corrected permutation test corrected for gene length P < 1 × 10−5, statistics in Supplementary Table S8). The 65 genes (57 gene symbols) shared across all 3 NDDs are shown below. Genes that are known genetic risk factors for ASD or ID are shown in bold (both ASD and ID), underlined (ASD only), or italics (ID only). Genes differentially expressed (DE) or with differential transcript usage (DT) are shown in red for ASD and SCZ, blue for ASD only, and purple for SCZ only. (B) DMR associated genes are significantly enriched (P-values <0.05 for gene length corrected null distribution permutation testing; see Methods) for genes associated with ASD genetic risk (ASD Missense Mutations Recurrent and SAFARI ASD lists). DMR associated genes are significantly enriched for genes with altered gene expression in numerous neurodevelopmental, neuropsychiatric, and neurodegenerative disorders including ASD, SCZ, ADD, and BD. DEG, differentially expressed genes; SFARI, Simons Foundation Autism Research Initiative; SCZ, schizophrenia; BD, bipolar disorder; AAD, alcohol abuse disorder. Mutation Intolerant pLI > 0.9, probability of being loss-of-function >0.9 (top genes that are intolerant to human mutation) (Lek et al. 2016), paternally imprinted genes for humans from http://www.geneimprint.com, Nardone ASD DMR genes from (Nardone et al. 2017), and RTT human brain DEG: DEG from Lin et al. (2016). ASD < Ctrl DEG are a compilation of overlaps between DMR genes and DEG genes from ASD brain from several papers (Gupta et al. 2014; Parikshak et al. 2016; Gandal et al. 2018a, 2018b). SCZ < Ctrl and SCZ > Ctrl DGE and BD < Ctrl and BD > Ctrl DGE are a compilation of overlaps from Gandal et al. (2018a, 2018b). Individual gene list overlaps from each source as well as all gene lists, citations, and overlap statistics are in Supplementary Table S8.