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Table 1 Top 15 DEGs in CHD8+/− vs idiopathic ASD cerebral organoids

From: CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells

CHD8+/− Log2FC Padj Log2FC_11 FDR Log2FC_31 FDR
DLX6-AS1 5.34 3.85E-86 4.72 1.70E-75 4.61 7.03E-37
ARMCX1 −2.48 4.47E-34 NS NS NS NS
DLX1 3.84 5.97E-32 2.14 1.38E-11 1.35 8.69E-03
FZD8 2.21 1.17E-26 1.19 2.35E-04 NS NS
CPNE6 3.55 1.47E-24 NS NS NS NS
PAX6 2.03 2.05E-22 NS NS 1.29 2.23E-04
SLC1A3 1.61 2.05E-22 1.13 9.21E-06 NS NS
EOMES 3.10 9.04E-22 2.96 1.85E-17 2.79 1.17E-06
MPPED1 2.92 3.31E-21 1.57 4.50E-05 1.41 7.29E-03
COL25A1 2.67 4.42E-21 NS NS NS NS
SCGN 3.22 9.46E-20 2.15 1.25E-06 1.37 1.57E-02
STK17B 2.08 9.46E-20 NS NS NS NS
LIX1 2.14 8.70E-19 NS NS 0.83 2.53E-02
BCL11B 1.63 7.21E-18 0.95 4.85E-02 2.16 2.36E-12
SHISA2 2.14 2.29E-17 1.41 1.58E-06 NS NS
  1. Top 15 DEGs in CHD8 +/− are shown in left columns with fold change (FC) and p value adjusted for genome-wide significance (padj). The right columns show the FC and false discovery rate (FDR) values for the same genes, derived from the Mariani et al. study [42]. Log2FC_11 is from day 11 cerebral organoids, while log2FC_31 is from day 31 organoids. Note that DLX6-AS1 was the top DEG in day 11 organoids and the 6th top DEG in day 31 organoids