Table 1.
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.