Table 1.

Microarray Data Showing the Effect of JQ1 on Expression of Selected Genes

Gene function	Gene (selected genes shown)	Rank total genes on array=30,854)	Control Av. gene expression	JQ1 Av. gene expression	(−)-JQ1 Av. gene expression	Log2 change JQ1 vs control (+up; −down)	% change gene expression JQ1 vs control	Benjamini–Hochberg derived q-values for multiple testing
Pluripotency genes	Nanog	24	699	207	740	−1.753	70.3% down	N/A
	Fbx15	7	1,321	279	1,256	−2.245	78.9% down	q=1.6×10−3
	Rex1	55	1,113	482	1,275	−1.206	56.7% down	q=0.02
Embryonic patterning genes	Lefty1	1	706	87	676	−3.028	87.7% down	q=7.1×10−4
	Lefty2	29	234	78	187	−1.585	66.7% down	q=3.4×10−3
	Nodal	139	568	310	610	−0.873	45.4% down	q=0.008
Bromodomain BET family genes	Brd4	30,345	184	252	181	+0.451	36.7% up	q>0.05
	Brd2	30,832	497	1,084	482	+1.125	118.0% up	q=0.006
	Brd3	29,011	554	635	545	+0.195	14.5% up	q>0.05
	Brdt	20,820	79	80	79	+0.020	1.4% up	N/S
Pluripotency core transcriptional genes	Oct4	318	3,284	2,092	3,544	−0.651	36.3% down	q=0.05
	Sox2	27,978	129	139	126	+0.114	8.2% up	N/S
	Klf4	1,312	122	101	122	−0.007	17.2% down	N/S
	Mof	30,380	293	404	301	+0.466	37.9% up	q=0.01
	Myc	27,965	83	90	84	+0.113	8.1% up	N/S

Transcriptional profiling was performed using the Illumina microarray platform. ESCs were exposed to JQ1 or (−)-JQ1 or vehicle only for 16 h in independent quadruplicate experiments. Average gene expression data is shown with log change for JQ1 versus control and t-test. Percentage up or downregulation of the gene has been calculated and the P values have been subjected to a Benjamini–Hochberg correction for multiple testing of genes other than Nanog (N/A=not applicable; N/S=not significant). Lefty1 was the most downregulated gene. Selected other genes are shown, including ESC core transcriptional factors, BET protein family members, and various genes involved with embryonic patterning and pluripotency.

ESC, embryonic stem cell; BET, bromodomain and extraterminal domain.