Table 2. Top 30 significant genes with differential DNA methylation between NFAs and FAs.

Gene_Symbol	Probe_CpGa	Target	NFA-M	SDb	FA-M	SD	NFA-FAc	p-value	FDRd
KCNAB2	cg18192083*	TSS200e	0.77	0.11	0.06	0.02	0.71	1.33×10−15	5.11×10−10
CIITA	cg09015246	1stExon	0.76	0.13	0.13	0.04	0.63	3.44×10−14	6.60×10−9
SPAG17	cg12435551	Body	0.77	0.15	0.06	0.05	0.7	6.15×10−14	7.87×10−9
TFAP2E	cg22851880	TSS1500f	0.79	0.14	0.13	0.05	0.66	2.02×10−13	1.94×10−8
KCNAB2	cg03400374*	TSS200	0.79	0.1	0.08	0.06	0.71	7.27×10−13	4.65×10−8
SOCS1	cg10784813*	3′UTR	0.7	0.15	0.16	0.06	0.53	1.88×10 −11	8.03×10−7
KCNAB2	cg12604162*	TSS1500	0.74	0.11	0.13	0.06	0.62	2.43×10−11	8.49×10−7
NME9	cg05652381	5′UTR	0.23	0.2	0.86	0.05	−0.63	3.46×10−11	1.11×10−6
SNORD115-48	cg27513586	TSS1500	0.52	0.11	0.15	0.03	0.37	4.15×10−11	1.14×10−6
TFAP2E	cg13558810	TSS1500	0.7	0.17	0.15	0.04	0.55	4.11×10−11	1.21×10−6
SNTG1	cg21177502	5′UTR	0.75	0.16	0.25	0.05	0.5	1.56×10−10	2.85×10−6
PSEN2	cg05134019	5′UTR	0.23	0.17	0.81	0.07	−0.58	1.21×10−10	2.91×10−6
TFAP2E	cg26372517	5′UTR	0.71	0.2	0.08	0.03	0.64	1.52 ×10−10	2.92×10−6
FAM26D	cg12354014	5′UTR	0.57	0.14	0.13	0.05	0.44	1.30×10−10	2.94×10−6
NEAT1	cg14758218	Body	0.68	0.2	0.05	0.01	0.64	1.70×10−10	2.97×10−6
TNFRSF11A	cg16174779	Body	0.74	0.18	0.16	0.07	0.58	1.49×10−10	3.02×10−6
UNC5A	cg03320873	Body	0.75	0.21	0.16	0.05	0.59	2.00×10−10	3.34×10−6
MERTK	cg06682024	Body	0.61	0.17	0.09	0.03	0.52	2.47×10−10	3.80×10−6
CAPN2	cg06756211*	Body	0.7	0.23	0.04	0.05	0.66	2.44×10−10	3.90×10−6
MDN1	cg27302675	Body	0.24	0.22	0.88	0.06	−0.64	2.77×10−10	3.94×10−6
PIK3R1	cg24797508*	Body	0.63	0.18	0.09	0.06	0.54	2.68×10−10	3.95×10−6
PCSK6	cg10845124	Body	0.37	0.16	0.86	0.02	−0.49	3.33×10−10	4.26×10−6
KCNQ4	cg15867428	Body	0.56	0.17	0.08	0.05	0.48	4.12×10−10	4.39×10−6
PHLDB1	cg08473858	TSS1500	0.66	0.18	0.15	0.04	0.51	4.05×10−10	4.57×10−6
SLC7A5	cg08617020	Body	0.73	0.14	0.32	0.04	0.41	3.72×10−10	4.61×10−6
LGALS3	cg02183170	TSS200	0.74	0.18	0.14	0.08	0.6	4.02×10−10	4.68×10−6
SEMA5B	cg04830808	5′UTR	0.52	0.15	0.09	0.04	0.43	3.99×10−10	4.78×10−6
AEBP1	cg08739576	1stExon	0.22	0.06	0.06	0.01	0.16	5.12×10−10	4.91×10−6

^aProbe_CpG: the Illumina HM450 probe ID.

^bSD: standard deviation.

^cNFA-FA: the mean beta value subtractive difference between NFA tumors and FA tumors.

^dFDR: False Discovery Rate.

^eTSS200: 200 bp within transcription start site.

^fTSS1500: 1500 bp within the transcription start site.

* Promoter Associated.

Link to the whole information of the Probe_CpG: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534.