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. Author manuscript; available in PMC: 2015 Jul 2.
Published in final edited form as: Neuron. 2014 Jul 2;83(1):69–86. doi: 10.1016/j.neuron.2014.05.035

Figure 6.

Figure 6

phNPC preserved modules are enriched in ASD associated genes. (A) In vivo defined modules preserved in differentiating phNPCs were tested for enrichment of disease associated genes from a curated list of autism-associated genes (ASD SFARI; (Banerjee-Basu and Packer, 2010)), rare de-novo protein disrupting mutations found in ASD and siblings (Iossifov et al., 2012; Neale et al., 2012; O’Roak et al., 2012; Sanders et al., 2012), two ASD associated modules defined in post-mortem brain (asdM12 and asdM16; (Voineagu et al., 2011)), a curated list of genes associated with intellectual disability (ID All) (Inlow and Restifo, 2004; Lubs et al., 2012; Parikshak et al., 2013; Ropers, 2008; van Bokhoven, 2011), the intersection of ASD SFARI with ID (ASD-ID overlap), the relative complement of these (ASD only, ID only), a list of genes disrupted by CNVs in schizophrenia (Levinson et al., 2011), genes near significantly associated loci in GWAS of schizophrenia (Ripke et al., 2013), and genes near significantly associated loci in GWAS of late onset Alzheimer’s disease (Naj et al., 2011). Enrichment was assessed using Fisher’s exact test and the FDR (Benjamini and Hochberg, 1995) correction for multiple comparisons P-value is displayed. (B) Protein disrupting de novo SNVs found in ASD are enriched in the preserved midnightblue module. The correlation of each gene to the module eigengene (kME) is shown for in vivo and phNPC data (1 and 4 wk PD). ASD-associated genes are highlighted in red. Genes close to the solid red line (y=x) have the same kME in vivo and in vitro. The dotted red line represents an in vivo kME value 3 times less than observed in vivo. (C) Several genes that contain ASD-associated de novo SNVs have similar expression patterns in vivo and in vivo. (D) kME is shown for in vivo and phNPC data (1, 4, 8, and 12 wk PD) for the preserved salmon module that is enriched in asdM12 genes (Voineagu et al., 2011). ASD-associated genes in asdM12 are in red and are labeled. (E) Several asdM12 genes show similar expression patterns in vivo and in vitro.