Table 1 Contingency tables of observed and expected number of genes differentially expressed (correlating and anti-correlating), and genes with no difference in expression for ranges of differential methylation between non-seminoma and seminoma cell lines

Δβ	SEM/YST		No difference Observed	No difference Expected	YST/SEM		Total	P value	Significance
	Genes >2-fold	Genes >2-fold			Genes >2-fold	Genes >2-fold		Χ² (2df)
	Observed	Expected			Observed	Expected
0.9–0.95	2	0.75	2	2.86	0	0.39	4	0.2537
0.85–0.9	3	1.31	4	5.01	0	0.68	7	0.2157
0.8–0.85	16	5.42	10	20.75	3	2.82	29	0	***
0.75–0.8	16	4.86	8	18.6	2	2.53	26	0	***
0.7–0.75	16	5.61	9	21.47	5	2.92	30	0	***
0.65–0.7	11	5.42	16	20.75	2	2.82	29	2.93E−02	*
0.6–0.65	12	6.55	21	25.04	2	3.41	35	5.57E−02
0.55–0.6	7	5.05	17	19.32	3	2.63	27	0.5819
0.5–0.55	13	7.67	26	29.34	2	3.99	41	0.0789
0.45–0.5	15	9.17	30	35.06	4	4.77	49	0.1018
0.4–0.45	21	10.66	29	40.79	7	5.55	57	0.001	***
0.35–0.4	16	13.66	49	52.23	8	7.11	73	0.6998
0.3–0.35	29	16.46	47	62.97	12	8.57	88	0.0006	***
0.25–0.3	29	20.02	64	76.56	14	10.42	107	0.0257	*
0.2–0.25	40	28.43	90	108.76	22	14.81	152	0.0033	**
0.15–0.2	34	34.98	128	133.8	25	18.22	187	0.2458
0.1–0.15	57	50.88	185	194.62	30	26.49	272	0.4326
0.05–0.1	96	78.57	279	300.52	45	40.91	420	0.0545
0–0.05	339	466.53	1,939	1,784.54	216	242.93	2,494	0.00E+00	***
Total	772	772	2,953	2,953	402	402	4,127

Δβ	SEM/TERT		No difference Observed	No difference Expected	TERT/SEM		Total	P value	Significance
	Genes >2-fold	Genes >2-fold			Genes >2-fold	Genes >2-fold		Χ² (2df)
	Observed	Expected			Observed	Expected
0.9–0.95	0	0	0	0	0	0	0	0
0.85–0.9	2	0.72	2	2.83	0	0.45	4	0.2225
0.8–0.85	6	2.5	8	9.9	0	1.58	14	0.0327	*
0.75–0.8	7	1.61	2	6.37	0	1.02	9	0.00001	***
0.7–0.75	4	1.07	2	4.25	0	0.68	6	0.0072	**
0.65–0.7	6	3.04	9	12.03	2	1.93	17	1.61E−01
0.6–0.65	6	3.39	11	13.45	2	2.16	19	2.94E−01
0.55–0.6	3	3.22	12	12.74	3	2.04	18	0.776
0.5–0.55	6	4.11	14	16.28	3	2.61	23	0.537
0.45–0.5	6	4.47	17	17.69	2	2.84	25	0.6713
0.4–0.45	5	4.65	19	18.4	2	2.95	26	0.8387
0.35–0.4	8	4.83	14	19.11	5	3.06	27	0.0965
0.3–0.35	9	6.08	18	24.06	7	3.86	34	0.0642
0.25–0.3	9	10.55	40	41.76	10	6.69	59	0.38001
0.2–0.25	19	17.17	58	67.94	19	10.89	96	0.0214	*
0.15–0.2	30	24.49	90	96.96	17	15.54	137	0.3921
0.1–0.15	33	42.38	172	167.73	32	26.89	237	0.2064
0.05–0.1	72	71.7	279	283.8	50	45.49	401	0.7676
0–0.05	245	270.01	1,117	1,068.69	148	171.31	1510	0.0216	*
Total	476	476	1,884	1,884	302	302	2,662

Δβ	SEM/EC		No difference Observed	No difference Expected	EC/SEM		Total	P value	Significance
	Genes >2-fold	Genes >2-fold			Genes >2-fold	Genes >2-fold		Χ² (2df)
	Observed	Expected			Observed	Expected
0.9–0.95	0	0	0	0	0	0	0	0
0.85–0.9	2	0.29	0	1.5	0	0.19	2	0.0031	**
0.8–0.85	10	2.51	7	12.79	0	1.69	17	1.60E−06	***
0.75–0.8	11	2.66	7	13.54	0	1.79	18	1.76E−07	***
0.7–0.75	11	3.25	10	16.55	1	2.19	22	0.00002	***
0.65–0.7	7	4.14	17	21.07	4	2.79	28	0.1935
0.6–0.65	5	3.55	17	18.06	2	2.39	24	6.97E−01
0.55–0.6	6	4.73	23	24.08	3	3.19	32	0.8183
0.5–0.55	11	6.06	29	30.85	1	4.09	41	0.0393	*
0.45–0.5	6	4.88	20	24.83	7	3.29	33	0.0682
0.4–0.45	7	5.32	26	27.09	3	3.59	36	0.7149
0.35–0.4	5	6.06	33	30.85	3	4.09	41	0.7312
0.3–0.35	8	9.9	51	50.41	8	6.68	67	0.729
0.25–0.3	11	13.15	68	66.97	10	8.88	89	0.7749
0.2–0.25	21	16.7	74	85.02	18	11.27	113	0.0378	*
0.15–0.2	20	18.03	85	91.79	17	12.17	122	0.2681
0.1–0.15	32	32.96	169	167.79	22	22.25	223	0.9805
0.05–0.1	56	59.86	298	304.73	51	40.41	405	0.2045
0–0.05	288	322.94	1,698	1,644.06	199	218	2,185	0.0272	*
Total	517	517	2,632	2,632	349	349	3,498

Abbreviations: EC, embryonal carcinoma; df, degree of freedom; SEM, seminoma; TERT, teratoma; YST, yolk sac tumour. P values of the Χ²-test of association between methylation and expression are given. *P<0.05

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