Table 2.

List of top 30 most highly significantly differentially expressed genes, which were also significantly differentially methylated distinguishing TNBC from non-TNBC, along with number of DNA methylation (DM) sites per gene and estimates of differential expression and differential methylation p-values. All p-values were adjusted for the false discovery rates.

Gene_Symbol	Chromosome Position	EXP-Value	DM_Sites	DM p-Value
PTPRN2	7q36.3	1.08 × 10−15	487	1.69 × 10−19
PCDHGA1	5q31	4.49 × 10−2	242	1.36 × 10−22
MSLN	16p13.3	2.86 × 10−8	165	1.50 × 10−24
CBFA2T3	16q24.3	8.05 × 10−12	146	4.07 × 10−25
CUX1	7q22.1	1.01 × 10−3	120	8.13 × 10−28
ANKRD11	16q24.3	2.92 × 10−5	114	3.40 × 10−21
NCOR2	12q24.31	1.97 × 10−2	112	1.07 × 10−27
LMF1	16p13.3	1.62 × 10−14	111	9.23 × 10−27
ABR	17p13.3	1.32 × 10−3	103	1.39 × 10−24
SLC45A4	8q24.3	1.12 × 10−4	103	3.29 × 10−31
SYNGAP1	6p21.32	5.78 × 10−6	99	2.34 × 10−20
TP73	1p36.32	2.26 × 10−6	96	2.27 × 10−25
PRKAR1B	7p22.3	9.45 × 10−3	95	3.32 × 10−27
ADAMTS2	5q35.3	1.47 × 10−2	86	1.07 × 10−28
PRRT1	6p21.32	3.99 × 10−7	86	1.63 × 10−26
PCDHA2	5q31.3	1.09 × 10−3	83	2.04 × 10−10
ANK1	8p11.21	5.84 × 10−3	82	1.75 × 10−25
TBC1D16	17q25.3	5.65 × 10−3	81	3.31 × 10−31
HOOK2	19p13.13	1.31 × 10−4	79	3.86 × 10−23
COL23A1	5q35.3	2.15 × 10−5	75	1.10 × 10−34
NFATC1	18q23	1.38 × 10−2	75	9.25 × 10−33
FOXK1	7p22.1	2.74 × 10−5	73	4.24 × 10−33
BCOR	Xp11.4	1.09 × 10−7	72	2.95 × 10−21
COL4A2	13q34	3.03 × 10−2	72	5.02 × 10−25
PCDHA4	5q31.3	2.16 × 10−5	72	2.04 × 10−10
RGS12	4p16.3	3.48 × 10−8	71	1.21 × 10−31
RGL2	6p21.32	1.31 × 10−14	69	4.34 × 10−29
DNAH17	17q25.3	1.22 × 10−4	68	1.74 × 10−26
CTBP2	10q26.13	1.51 × 10−4	67	6.16 × 10−26
HOXC4	12q13.13	1.60 × 10−9	67	3.63 × 10−11