Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors

Table 2 Top-ranked differentially methylated CpGs in T2E-fusion-positive versus T2E-fusion-negative prostate tumors

CpG ID	Chromosome	Gene	Location	CpG island	Mean β T2E-negative	Mean β T2E-positive	Mean β difference	Q-value
Hypermethylation
cg11258089	5	PDE4D	Body; TSS200	Yes	0.20	0.53	0.33	1.19E−51
cg22706610	5	PDE4D	Body; TSS200	Yes	0.22	0.50	0.28	1.19E−51
cg26870744	5	PDE4D	Body; TSS200	Yes	0.17	0.43	0.27	1.19E−51
cg07190535	5	PDE4D	Body; TSS1500	Yes	0.26	0.53	0.27	1.57E−50
cg08554295	5	PDE4D	Body; TSS1500	No	0.18	0.46	0.29	1.57E−50
cg16261871	5	PDE4D	Body; TSS200	Yes	0.25	0.52	0.28	2.83E−46
cg19694010	12	–	IGR	Yes	0.19	0.45	0.27	3.45E−46
cg15044248	17	SEPT9	TSS200; 5′ UTR; body	Yes	0.11	0.38	0.26	7.05E−46
cg14087806	17	–	IGR	Yes	0.19	0.49	0.30	7.05E−46
cg06848185	17	SEPT9	TSS1500; 5′ UTR; body	Yes	0.10	0.36	0.26	3.84E−45
cg13468945	17	–	IGR	Yes	0.19	0.47	0.29	4.20E−43
cg08378505	17	NT5C	Body	Yes	0.15	0.45	0.30	3.41E−40
cg17300544	17	SEPT9	TSS200; 5′ UTR; body	Yes	0.18	0.47	0.29	7.49E−39
cg26896572	3	C3orf14	TSS1500	Yes	0.26	0.53	0.27	2.28E−38
cg21454031	17	–	IGR	No	0.22	0.48	0.26	5.03E−38
cg10520594	17	NT5C	Body	Yes	0.19	0.44	0.25	9.43E−38
cg15059608	3	C3orf14	TSS1500	No	0.32	0.58	0.25	3.36E−31
cg21869055	19	KLK10	5′ UTR	Yes	0.26	0.51	0.25	3.06E−30
cg25623934	2	TRIB2	Exon 1; body	Yes	0.22	0.49	0.27	1.53E−29
Hypomethylation
cg08480458	3	CACNA1D	Body	Yes	0.47	0.15	0.32	5.42E−45
cg15473186	3	CACNA1D	Body	Yes	0.57	0.31	0.27	1.28E−44
cg06717750	16	RAB40C	Body	No	0.80	0.52	0.28	6.87E−43
cg12668309	3	CACNA1D	Body	Yes	0.33	0.08	0.26	4.18E−42
cg17312492	15	GREM1	5′ UTR	Yes	0.43	0.17	0.26	7.96E−42
cg14337339	3	CACNA1D	Body	Yes	0.43	0.12	0.31	3.41E−40

The table shows differentially methylated CpGs (FDR Q-value <0.00001) that have a mean methylation (β-value) difference of at least 25 % between fusion-positive versus fusion-negative PCa
T2E TMPRSS2:ERG, TSS1500 200 to 1500 base pairs upstream of the transcription start site, TSS200 200 base pairs upstream of the transcription start site, UTR untranslated region, IGR intergenic region

ISSN: 1868-7083