Table 3.

Changes in dup15q DPSC neurons overlap changes seen in postmortem cortex in both dup15q and idiopathic ASD

Fold enrichment (P value)		↑ in Dupl5q cortex	↓ in Dupl5q cortex	↑ In idiopathic ASD cortex	↓ In idiopathic ASD cortex
All genes	↑ 1500 in DPSC neurons	1.41 (le-6)	1.06 (0.5)	1.25 (0.05)	1.14 (0.3)
	↓ 1500 in DPSC neurons	0.87 (0.1)	0.95 (0.6)	0.97 (0.8)	1.07 (0–6)
All genes except 15qll-13 genes	↑ 1500 in DPSC neurons	1.37 (le-5)	1.07 (0.4)	1.26 (0.04)	1.09 (0.5)
	↓ 1500 in DPSC neurons	0.88 (0.1)	0.95 (0.6)	0.96 (0.8)	1.08 (0.5)

In each cell is the fold enrichment of the overlap between the gene sets denoted by the corresponding row and column, and the two-tailed p value is given in parenthesis (computed using the Fisher’s exact function in scipy.stats). Columns denote genes significantly differentially expressed in postmortem cortex between either Dup15q and controls or idiopathic ASD and controls at a False Discovery Rate of 5%. Rows denote the 1500 most upregulated genes by p value and the 1500 most downregulated genes by p value in DPSC neurons comparing Dup15q DPSC neurons to control DPSC neurons (this was chosen to reduce type II error given the limited power of the DESeq analyses on these sample sizes). This is repeated excluding all genes in the 15q11-13 cytobands (which also excludes some genes flanking the duplicated region). The background was the intersection of genes expressed in Parikshak et al. and genes assigned a p value by DESeq in this study