Table 3. Differentially expressed genes in prostate tissue specimens of patients with or without progression to BCR based on expression in tumor only and ratio of expression in tumor vs. normal.

	Tumor only					Tumor vs Normal
	Probe	p value	q-value	Expected FP	BCR vs Non-BCR	Probe	p value	q-value	Expected FP	BCR vs Non-BCR
1	ERG8	3.50E-05	0.00287	0.003	↓	Pan.ERG	0.00025	0.01594	0.016	↓
2	ERG1.ERG2.ERG3	0.00012	0.00505	0.010	↓	ERG8	0.00036	0.01594	0.032	↓
3	Pan.ERG	0.00036	0.00951	0.029	↓	ERG1.ERG2.ERG3	0.00124	0.03686	0.111	↓
4	GGT1	0.00046	0.00951	0.038	↓	T2. ERG.exon4.fusion	0.00342	0.06245	0.250	↓
5	HDAC1	0.00158	0.02542	0.127	↓	TP53	0.00349	0.06245	0.312	↓
6	KLK2	0.00197	0.02542	0.153	↓	HDAC1	0.00575	0.08562	0.514	↓
7	MYO6	0.00214	0.02542	0.178	↓	NCOA2	0.01971	0.24723	1.731	↑
8	PLA2G7	0.00283	0.02941	0.235	↓	VEGFA	0.02213	0.24723	1.978	↑
9	T2.ERG.exon4.fusion	0.00319	0.02947	0.265	↓	PTEN	0.03389	0.30341	2.731	↓
10	BICD1	0.00509	0.04225	0.422	↓	ACPP	0.03911	0.30341	3.034	↑
11	CACNA1D	0.00993	0.07502	0.825	↓	KLF4	0.04010	0.30341	3.337	↑
12	ACPP	0.02298	0.15908	1.909	↑	TMPRSS2	0.04074	0.30341	3.641	↑
13	FAS	0.03467	0.22155	2.880	↓	FAS	0.04674	0.32132	4.177	↓
14	T2.ERG.exon2.fusion	0.03828	0.22718	3.180	↓	HSP27	0.06458	0.39413	5.518	↑
15	C.MYC	0.06511	0.34971	5.246	↓	T2.ERG.exon2.fusion	0.06616	0.39413	5.912	↓