Table 1.

Gene ontology enrichment analysis of the 197 genes commonly showing significant differences in DNA methylation levels between non-cancerous and cancerous tissue specimens in two or more driver aberration groups, for which DNA methylation alterations would potentially result in mRNA expression alterations (listed in Supplementary Table 8A, available at Carcinogenesis Online), according to protein function using MetaCore software

Protein class	r	n	R	N	Expected	Ratio	P
Transcription factors	32	220	1254	40 677	6.782	4.718	3.734E−13
Enzymes	36	220	2869	40 677	15.52	2.32	2.016E−06
Receptors	19	220	1700	40 677	9.194	2.066	2.367E−03
Kinases	9	220	685	40 677	3.705	2.429	1.279E−02
Ligands	5	220	562	40 677	3.04	1.645	1.898E−01
Phosphatases	2	220	242	40 677	1.309	1.528	3.769E−01
Proteases	4	220	623	40 677	3.369	1.187	4.358E−01
Other	115	220	32 813	40 677	177.5	0.648	1.534E−21

r, number of objects from the present data set for a given protein class; n, total number of objects from the present data set; R, number of background objects from the database for a given class; N, total number of background objects from the database; Expected, mean value for hypergeometric distribution (n × R/40 677); Ratio, the ratio of actual/expected. If the ratio is more than 1, P values less than 0.0001 mean significant enrichment, and these are bold.