TABLE II.

Genes responsible for epigenetic modifications (epigenetic effectors) significantly dysregulated in all 3 RT subsets (AT/RT Cluster1-3-4, AT/RT Cluster 2, KRT) compared to normal.

Gene	Member of	Dir in RTs	AT/RT 134 P-value	AT/RT 134 FC	AT/RT 2 P-value	AT/RT 2 FC	KRT P-value	KRT FC
ACTL6A	Trithorax (SWI/SNF)	Up	1.77E-11	10.3	5.95E-08	10.3	4.25E-08	4.9
ARID1A	Trithorax (SWI/SNF)	Up	1.42E-07	2.6	1.94E-09	3.7	8.46E-08	2.8
ASF1B		Up	2.38E-06	10.6	1.01E-06	8.2	3.28E-08	4.9
BAZ1A	Trithorax (ISWI)	Up	3.37E-06	6.0	3.63E-09	14.5	5.60E-05	3.4
CBX7	Polycomb (PRC1)	Down	2.69E-11	0.02	1.58E-10	0.04	8.49E-07	.10
CHD1L	Trithorax	Up	7.00E-04	2.1	1.14E-03	2.2	2.05E-12	4.8
CHD4	Trithorax	Up	4.53E-04	2.4	6.52E-05	3.4	7.38E-04	2.9
EZH2	Polycomb (PRC2)	Up	2.96E-10	30.7	2.05E-09	108.0	4.40E-12	17.3
HAT1		Up	2.17E-04	2.4	7.83E-04	2.2	6.32E-04	2.0
HDAC2		Up	2.92E-07	2.3	3.94E-06	3.4	2.22E-06	3.8
HELLS	Trithorax	Up	9.85E-05	5.1	1.55E-05	18.0	9.64E-11	15.2
HMGA2		Up	1.64E-08	394.4	3.40E-04	70.4	3.49E-05	29.0
HMGB2		Up	4.37E-06	3.3	9.09E-09	7.0	1.75E-09	5.6
HMGN1		Up	2.27E-06	2.4	1.17E-06	3.4	2.66E-06	2.3
PCGF1	Polycomb (PRC1)	Up	2.62E-05	5.0	5.07E-04	5.3	1.00E-06	2.3
PHF21A		Up	5.06E-04	2.5	3.78E-04	2.6	1.34E-12	4.8
PRMT1		Up	7.35E-05	2.0	4.23E-08	2.8	2.06E-05	5.9
RBBP4	Both (PRC2)	Up	1.53E-04	2.2	3.59E-04	2.8	3.76E-05	4.2
SETDB1		Up	3.37E-06	2.9	7.98E-06	4.9	1.10E-05	2.1
SMARCAL1	Trithorax	Up	1.16E-05	2.9	9.68E-04	2.6	1.34E-07	2.4
SMARCC1	Trithorax (SWI/SNF)	Up	1.23E-08	4.7	3.02E-10	5.1	3.37E-06	2.7
SSRP1		Up	1.52E-05	2.2	1.82E-07	3.4	3.23E-07	4.1
WHSC1		Up	7.21E-06	3.4	1.50E-07	6.0	3.99E-10	6.5

FC = Fold Change