Table 1.

Differentially expressed and CHD8-bound genes associated with ASD and neurodevelopmental pathways

GeneASD listFC, knockdown/controlP value
Selected genes that are indirectly regulated by CHD8*
LAMA4−4.445.95 × 10−13
TIMP3−3.232.65 × 10−10
KCNJ10S/A−4.953.44 × 10−10
SCN2ABoth−7.313.85 × 10−9
SLIT1−4.881.38 × 10−8
MBD3S/A2.724.90 × 10−8
BAI1−3.252.40 × 10−7
SYTL4−3.452.79 × 10−7
GPX1S/A1.992.58 × 10−5
SOX9−2.083.33 × 10−5
HS3ST5S/A6.914.05 × 10−5
ACSBG1−2.166.88 × 10−5
SHANK3S/A1.872.39 × 10−4
EFHD1−2.872.66 × 10−4
LIFR−1.783.02 × 10−4
TESK2−2.414.03 × 10−4
HYDINS/A−3.307.09 × 10−4
PLXNA2−2.208.01 × 10−4
ANO5W−1.939.12 × 10−4
RIMS3S/A−1.739.64 × 10−4
KANK1S/A−1.749.95 × 10−4
Selected ASD-associated genes that are bound by CHD8
CHD8Both−2.563.62 × 10−9
NFKBIL1W2.027.61 × 10−5
CBX4W1.853.79 × 10−4
TCF3W1.691.17 × 10−3
SDC2S/A1.791.20 × 10−3
RAI1S/A1.691.57 × 10−3
SLITRK5S/A1.692.03 × 10−3
PTENS/A−1.813.00 × 10−3
ARHGAP2S/A2.675.33 × 10−3
OGTS/A−1.490.0111
RPS6KA2S/A−1.510.0114
TRIOS/A1.440.0424
ADKS/A−1.400.0430
LZTS2S/A1.390.0432
CBSS/A1.380.0437
POGZBoth−1.300.100
ARID1BBoth−1.200.264
MBD5Both−1.190.307
TRIP12Both−1.170.337
ADNPBoth−1.130.436
SETD2Both−1.050.757
SYNGAP1Both1.040.818
CUL3Both1.010.951
SUV420HBoth1.000.978
  • Both, genes in both the SFARI/AutismKB and Willsey et al. (26) lists; FC, fold change of gene in shRNA knockdowns compared with controls: A positive fold-change corresponds to up-regulation when CHD8 is knocked down; a negative-fold change corresponds to down-regulation (P values for differential expression are listed for each gene); S/A, genes in the ASD gene list from SFARI and AutismKB, as described in SI Materials and Methods; W, genes in the Willsey et al. (26) pASD or hcASD gene list. See Dataset S1 for all detectable genes and associated data.

  • * Genes that are strongly differentially expressed following CHD8 suppression (Benjamin–Hochberg q < 0.05) and lack CHD8-binding (i.e., that are indirectly regulated by CHD8). Genes shown are either ASD-associated genes or down-regulated genes associated with cell adhesion or neurodevelopmental pathways.

  • ASD-associated genes in which CHD8-binding sites were detected by all three antibodies (q < 0.05). Genes either were differentially expressed with a CHD8-binding site or were bound by CHD8 and found in both ASD gene sets described.

  • These genes met q < 0.05 for differential expression. FC, fold change of gene in shRNA knockdowns compared with controls. A positive fold-change corresponds to up-regulation when CHD8 is knocked down; a negative-fold change corresponds to down-regulation. P values for differential expression are listed for each gene.