Table 3. Comparison between methylation status and expression levels for genes in which these show significant correlation.

			Delta beta-value				% Tumour methylated
			1st cohort		2nd cohort		1st cohort		2nd cohort
Genes	Ave. LODs	Tumour expression	Germ	YST	Germ	YST	Germ	YST	Germ	YST
TFAP2C	28.71057	Germinoma	0.02692	0.50441	0.03356	0.38462	0	88	0	64
PYCARD	11.98783	Germinoma	0.02194	0.55576	0.06177	0.45505	0	100	0	91
HDAC9	9.563456	Germinoma	0.03521	0.31761	0.045	0.38154	0	38	0	55
ETV1	8.929844	Germinoma	0.04711	0.28954	0.17621	0.25473	0	38	11	36
CD2	8.079104	Germinoma	0.10937	0.52285	0.04331	0.41915	29	100	22	91
CASP8	7.686273	Germinoma	0.11408	0.41122	0.11146	0.40555	0	75	11	82
HPN	−7.431153	YST	0.14285	0.56466	0.16644	0.39917	29	100	22	82
EVI2A	4.376357	Germinoma	0.09123	0.38608	0.10608	0.3332	0	88	11	73
HLA-F	4.280225	Germinoma	0.0023	0.71691	0.01473	0.73472	0	100	0	73

Abbreviations: GCT=germ cell tumours; LOD=logarithm of odds; YST=yolk sac tum.

aveLODS represents the degree to which these genes are expressed at higher levels in germinomas than in YSTs (from Palmer et al (2008)). Methylation status is shown as the delta beta-value for difference in methylation between germinomas and YSTs in the two cohorts of GCTs analysed, and as a percentage of tumours in which the gene was significantly hypermethylated.