The file "gene_T_1.txt" contains EntrezGeneID of background genes for CHD8 target gene analysis.

The file "CHD8_bound.txt" contains EntrezGeneID of CHD8-bound genes.

The file "gene_T125_down.txt" contains EntrezGeneID of CHD8-activated genes at E12.5.

The file "gene_T145_down.txt" contains EntrezGeneID of CHD8-activated genes at E14.5.

The file "gene_T175_down.txt" contains EntrezGeneID of CHD8-activated genes at E17.5.

The file "gene_T21_down.txt" contains EntrezGeneID of CHD8-activated genes at P0.

The file "gene_T77_down.txt" contains EntrezGeneID of CHD8-activated genes at adult.

The file "gene_T125_up.txt" contains EntrezGeneID of CHD8-repressed genes at E12.5.

The file "gene_T145_up.txt" contains EntrezGeneID of CHD8-repressed genes at E14.5.

The file "gene_T175_up.txt" contains EntrezGeneID of CHD8-repressed genes at E17.5.

The file "gene_T21_up.txt" contains EntrezGeneID of CHD8-repressed genes at P0.

The file "gene_T77_up.txt" contains EntrezGeneID of CHD8-repressed genes at adult.

Code in this directory can be run as follows:

## Overlap between CHD8-activated/-repressed genes and CHD8-bound genes.

source("plot_overlap_bound.R")

## Overlap between CHD8-activated/-repressed genes and ASD genes with at least one dnLoF mutation.

source("plot_overlap_ASD.R")

## Expression changes of CHD8-activated and -repressed genes during the transition from vRG cells to IPCs at GW10.

source("calculate_FC_vRG_IPC.R")

source("plot_FC_vRG_IPC_GW10.R")

## Spearman’s correlation between CHD8-activated/-repressed genes and CHD8 during the transition.

source("cor_vRG_IPC_GW10.R")

source("calculate_cor_vRG_IPC_GW10.R")

source("plot_cor_vRG_IPC_GW10.R")

## Top GO terms enriched with CHD8-activated and -repressed genes.

source("GO.R")

source("plot_overlap_activated.R")

source("plot_overlap_repressed.R")
