SUPPLEMENTARY:

Epigenetic Silencing Mediated Through Activated PI3K/AKT Signaling in Breast Cancer

Tao Zuo, Ta-Ming Liu, Xun Lan, Yu-I Weng, Rulong Shen,

Fei Gu, Yi-Wen Huang, Sandya Liyanarachchi, Daniel E. Deatherage,

Pei-Yin Hsu, Cenny Taslim, Bhuvaneswari Ramaswamy, Charles L. Shapiro,

Huey-Jen L. Lin, Alfred S. L. Cheng, Victor X. Jin, and Tim H.-M. Huang

1 Table of Content:

1. Fig. S1. Elevated AKT1 kinase activity in myrAKT1- transfected MCF10A cells.

------page 4

2. Fig. S2. Genome-wide view of H3K27me3 in mammary epithelial cells.

------page 5

3. Fig. S3. Biological functions of PI3K/AKT- downstream genes. ------page 6

4. Fig. S4. Genomic maps of 40 genes. ------page 8

5. Fig. S5. Comparing DNA methylation levels of four CpG islands measured by

meDIP-qPCR and MassARRAY.------page 11

6. Fig. S6. Validation of DNA methylation by MBDCap-seq.------page 13

7. Table S1. Summary of H3K27me3 ChIP-seq data ------page 14

8. Table S2. Distribution of H3K27me3 in MCF10A genome ------page 14

9. Table S3. Genes (n=488) enriched with H3K27me3 and downregulated by

PI3K/AKT- signaling ------page 15

10. Table S4. Genes (n=1005) enriched with H3K27me3 but without downregulation

------page 26

11. Table S5. Genes (n=723) downregulated by PI3K/AKT- but without enrichment of

H3K27me3 ------page 45

2 12. Table S6. Summary of 21 breast cancer cell lines ------page 60

13. Table S7. Summary of in silico expression values of 180 genes in 21 breast cancer

lines and 4 normal human mammary epithelial samples (HMECs)

------page 62

14. Table S8. ChIP-qPCR of H3K27me3 in 21 breast cancer cell lines and 4 HMECs

------page 66

15. Table S9. meDIP-qPCR in 21 breast cancer lines, 4 HMECs and myrAKT1- or

Vector transfected MCF10A cells ------page 68

16. Table S10. PCR primers of 40 genes ------page 70

17. Table S11. Gene expression after drug treatment ------page 71

18. Table S12. RT-PCR primers of 40 genes ------page 75

19. Table S13. MassARRAY PCR primers of 4 genes ------page 76

20. Table S14. Summary of MBDCap-seq data ------page 76

21. Table S15. Differentially methylated genes (n=143) identified by MBDCap-seq

analysis .------page 76

22. Experimental procedures ------page 79

23. Reference ------page 80

3 SUPPLEMENTAL DATA:

Fig. S1. Elevated AKT1 kinase activity in myrAKT1- transfected MCF10A cells.

AKT1 kinase activity increased 4-fold in myrAKT1- transfected MCF10A compared with vector control cells.

4

Fig. S2. Genome-wide view of H3K27me3 in mammary epithelial cells.

Top 1% enrichment regions of H3K27me3 are indicated as bars in the figure, i.e., AKT1

(Red) and Vector (Green) transfected MCF10A. Disseminated bars were matched to corresponding locations at chromosome bands in each of 23 chromosomes in the human genome. H3K27me3 enrichment was identified by the ChIP-seq peak calling program, bin-base enrichment thresholds (BELT) algorithm (Frietze et al., 2010; Cited in main text), with a False Discovery Rate (FDR) less than 0.05.

5

Fig. S3. Biological functions of PI3K/AKT- downstream genes.

Functional analyses were performed using IPA (Ingenuity Pathway Analysis) software.

PI3K/AKT- downstream targets were divided into three sets according to their gene expression and H3K27me3 status shown in Figure1D. Then gene lists were uploaded to IPA for statistical analyses. Of 488 genes marked by H3K27me3 and downregulated by AKT1, 172 genes (Table S3) are related to cancer (p = 9.74 x 10−13), while p values

are 8.55 x 10−3 (19 of 1005 genes, Table S4) and 2.05 x 10−9 (207 of 723 genes, Table

S5) in other two groups respectively. As shown in figure, the y-axis indicates negative

exponent of the p-value, the results of three categories are ordered parallel within each

6 function. 12 biological functions shown in figure are most significant ones derived from the analysis of 488 genes.

7 Figure S4

8 Figure S4

9 Figure S4

Fig. S4. Genomic maps of 40 genes.

A total of 40 genes, as shown in Figure 3A, were subjected to meDIP- and ChIP-qPCR assays. As shown in the figure, genomic maps illustrate distribution of CpG sites

(vertical bars) and locations of PCR primers (head-to-head arrows) around TSS region

at each locus.

10 Figure S5

11 Fig. S5. Comparing DNA methylation levels of four CpG islands measured by

meDIP-qPCR and MassARRAY .

A, genomic maps show CpG islands at promoter regions of four genes, i.e., SFRP1,

HOXA5, HOXA9, and SYNE2. Transcription start sites (TSSs) and locations of PCR primers were indicated in maps. B, DNA methylation levels of these 4 genes in 20 breast cancer cell lines and 4 normal breast epithelial cell samples (Fig.3 and 4) were assessed by meDIP-qPCR and MassARRAY, respectively. Pearson's correlation analysis was conducted to compare methylation levels measured by these two methods.

The linear regression r-squared (r2) values were shown in figure. Methylation levels

measured at the SYNE2 CpG island show the strongest correlation.

12 Figure S6

Fig. S6. Validation of DNA methylation by MBDCap-seq.

Box plot represents DNA methylation of 180 loci identified in Fig. 2A. Two of loci were not found in the MBDCap-seq dataset. Methylation levels were assessed by MBDCap- seq in T-47D cells treated with DAC and/or LY294002. Significance of differences among drug treatments was determined by Student’s t-test. *P<0.05, **P<0.01.

13 a Table S1. Summary of H3K27me3 ChIP-seq data AKT1 Vector Subtracted Reads 40,585,026 27,308,019 - Mapped Reads 21,195,941 17,394,048 - Unique Mapped Reads 15,589,956 11,789,771 - Peaks (Top 1%) 12,113 9,743 11,577 Peaks (Top 2%) 27,688 19,229 20,656 Peaks (Top 10%) 130,709 130,075 122,727 Note: a) ChIP-Seq analysis is described in Experimental procedures.

a Table S2. Distribution of H3K27me3 in MCF10A genome AKT1 Vector Subtracted Gene desert (>100-kb) 43,104 44,129 42,081 5' distal (-100 to -4-kb) 20,553 19,821 18,030 5' TSS (-4 to 2-kb) 7,485 7,232 6,154 Intragenic 39,454 39,237 39,050 3' end (<10-kb) 4,168 3,936 3,682 3' distal (>10-kb) 15,945 15,720 13,730 Total 130,709 130,075 122,727 Note: a) Genome-wide distribution of top 10% H3K27me3 peaks were shown in table.

14 Table S3. Genes (n=488) enriched with H3K27me3 and downregulated by PI3K/AKT signaling

Expressio H3K27me3 Polycomb Gene b Affymetrix c d Cancer a Accession Chr. n folds peak targets in f Symbol (Strand) Prob_ID (AKT1 vs. (distance to e related ES cells Vector) TSS [bp]) A2ML1 NM_144670 12(+) 1564307_a_at -9.83 1950 ABCA12 NM_173076 2(-) 215465_at -25.70 1838 ABCA5 NM_018672 17(-) 213353_at -3.59 1223 Yes Yes ABCA8 NM_007168 17(-) 204719_at -6.52 1265 Yes Yes ABCC2 NM_000392 10(+) 206155_at -4.06 -1454 Yes ABHD4 NM_022060 14(+) 218581_at -1.90 1637 NM_001003 ABLIM1 10(-) 200965_s_at -1.78 1172 408 ACACB NM_001093 12(+) 49452_at -4.09 -715 ACPL2 NM_152282 3(+) 226925_at -4.11 -1331 Yes ADD3 NM_016824 10(+) 201753_s_at -3.66 -1176 Yes ADRB2 NM_000024 5(+) 206170_at -1.76 1660 Yes Yes AFTPH NM_203437 2(+) 222472_at -1.58 -395 AGA NM_000027 4(-) 204333_s_at -1.63 918 AGPAT4 NM_020133 6(-) 228667_at -2.70 1924 AKR1C3 NM_003739 10(+) 209160_at -1.75 1127 Yes NM_001031 ALDH3A2 17(+) 202054_s_at -1.74 507 806 ALOX5AP NM_001629 13(+) 204174_at -2.41 -1493 AMOTL1 NM_130847 11(+) 225450_at -1.71 1221 AMY2B NM_020978 1(+) 228023_x_at -1.71 -590 Yes ► ANKRA2 NM_023039 5(-) 218769_s_at -1.85 -716 ANKRD38 NM_181712 1(-) 229125_at -3.83 -1945 Yes ANXA3 NM_005139 4(+) 209369_at -2.23 -63 AP1M2 NM_005498 19(-) 65517_at -4.80 957 ARHGAP29 NM_004815 1(-) 1558280_s_at -4.70 867 Yes ARHGAP8 NM_181335 22(+) 37117_at -7.57 -362 Yes ARL6IP NM_015161 16(-) 211935_at -2.21 1448 Yes ARRDC3 NM_020801 5(-) 224797_at -2.72 1410 ASAH1 NM_004315 8(-) 213702_x_at -1.55 -1898 Yes ASPM NM_018136 1(-) 219918_s_at -2.57 -247 ASS1 NM_000050 9(+) 207076_s_at -3.78 -905 Yes ATP9A NM_006045 20(-) 212062_at -11.16 -1497 ATXN1 NM_000332 6(-) 203232_s_at -5.25 533 ► AUH NM_001698 9(-) 205052_at -1.76 1882 AYTL1 NM_017839 16(+) 227889_at -1.81 -1716 B3GALTL NM_194318 13(+) 227083_at -1.50 -568 BAMBI NM_012342 10(+) 203304_at -2.86 -1594 Yes Yes BBX NM_020235 3(+) 223135_s_at -1.60 -1856 BDH2 NM_020139 4(-) 218285_s_at -1.74 1924 NM_001007 BRWD1 21(-) 231960_at -1.62 413 246 BSDC1 NM_018045 1(-) 218004_at -1.75 -247 BTG1 NM_001731 12(-) 200920_s_at -1.73 -134 ► BTG2 NM_006763 1(+) 201236_s_at -1.61 1429 Yes Yes

15 BTN3A3 NM_006994 6(+) 204821_at -3.08 1504 C10orf58 NM_032333 10(+) 224435_at -6.47 -514 C14orf1 NM_007176 14(-) 202562_s_at -1.82 1265 C14orf143 NM_145231 14(-) 214264_s_at -1.83 410 C14orf45 NM_025057 14(+) 220173_at -1.61 -1085 C15orf23 NM_033286 15(+) 225300_at -1.63 -594 Yes C1orf116 NM_023938 1(-) 219476_at -20.58 269 C1RL NM_016546 12(-) 218983_at -2.64 -215 C20orf19 NM_018474 20(+) 228291_s_at -2.69 -1287 C3orf40 NM_144635 3(+) 221904_at -1.91 585 C5orf26 NM_053000 5(+) 225698_at -2.41 235 C6orf85 NM_021945 6(-) 223194_s_at -2.18 780 C9orf3 NM_032823 9(+) 212848_s_at -1.50 -597 Yes C9orf72 NM_145005 9(-) 225919_s_at -1.74 -677 ► CA2 NM_000067 8(+) 209301_at -7.53 1168 Yes CA8 NM_004056 8(-) 220234_at -6.83 -1024 CALCOCO NM_020898 12(-) 209002_s_at -1.94 -1480 1 CALD1 NM_033157 7(+) 205525_at -3.10 -335 Yes CAMK2D NM_172115 4(-) 225019_at -1.69 -27 Yes CAP2 NM_006366 6(+) 212551_at -1.68 -681 Yes Yes CARD10 NM_014550 22(-) 210026_s_at -2.08 -2 Yes CBARA1 NM_006077 10(-) 216903_s_at -2.20 -1526 CCDC109A NM_138357 10(+) 225320_at -1.59 521 CCDC45 NM_138363 17(+) 225705_at -1.66 521 CCDC80 NM_199512 3(-) 225242_s_at -1.68 957 CCNB1 NM_031966 5(+) 228729_at -2.60 -1056 Yes CCNB2 NM_004701 15(+) 202705_at -2.81 -1875 Yes CD109 NM_133493 6(+) 239719_at -1.76 1588 Yes CD24 FJ226006 6(+) 216379_x_at -1.74 -653 Yes CD55 NM_000574 1(+) 201925_s_at -1.98 -1124 Yes CDK19 NM_015076 6(-) 212899_at -1.90 1860 Yes CDH17 NM_004063 8(-) 206517_at -5.37 -1024 Yes CDR2L NM_014603 17(+) 213230_at -1.88 -146 CDRT4 NM_173622 17(-) 228482_at -2.95 -1034 NM_001042 CENPA 2(+) 204962_s_at -1.92 1716 Yes 426 CENPE NM_001813 4(-) 205046_at -1.75 1533 CENTD1 NM_015230 4(-) 213618_at -7.91 -1720 CEP110 NM_007018 9(+) 205642_at -2.31 1253 CEP68 NM_015147 2(+) 212675_s_at -1.93 1100 CEP70 NM_024491 3(-) 238154_at -1.82 -424 Yes CHD3 NM_005852 17(+) 208806_at -1.81 -1953 CHMP2B NM_014043 3(+) 202537_s_at -1.58 -24 CHMP4C NM_152284 8(+) 226803_at -2.96 1931 CITED2 NM_006079 6(-) 209357_at -2.34 530 CLCA2 NM_006536 1(+) 206166_s_at -24.47 27 CLCN3 NM_173872 4(+) 201734_at -1.58 -176 Yes CLDND1 NM_019895 3(-) 208925_at -1.63 -786 CLK4 NM_020666 5(-) 228751_at -2.11 669 Yes CLU NM_203339 8(-) 222043_at -2.64 -128 Yes

16 CNKSR3 NM_173515 6(-) 225474_at -2.14 1838 COBLL1 NM_014900 2(-) 203642_s_at -2.64 1787 Yes Yes COL12A1 NM_080645 6(-) 225664_at -2.08 1436 Yes Yes COL27A1 NM_032888 9(+) 225293_at -1.63 -912 Yes COL3A1 NM_000090 2(+) 201852_x_at -14.11 927 Yes COL4A4 NM_000092 2(-) 229779_at -19.85 915 Yes Yes COL4A6 NM_033641 X(-) 213992_at -2.52 -3858 Yes Yes COL5A2 NM_000393 2(-) 221730_at -2.18 -1454 CPEB4 NM_030627 5(+) 224828_at -2.21 82 Yes CRBN NM_016302 3(-) 222533_at -1.73 1508 CREBBP NM_004380 16(-) 228177_at -1.63 -1898 Yes CREG1 NM_003851 1(-) 201200_at -2.00 -1090 Yes ► CROT NM_021151 7(+) 204573_at -2.27 385 CSF1R NM_005211 5(-) 203104_at -1.93 654 Yes CSGALNA NM_018371 8(-) 219049_at -1.90 -107 CT1 ► CSRP2 NM_001321 12(-) 207030_s_at -1.52 -1209 Yes ► CST6 NM_001323 11(+) 206595_at -8.47 -1209 Yes ► CTGF NM_001901 6(-) 209101_at -1.74 1990 Yes Yes CTSL2 NM_001333 9(-) 210074_at -6.51 -1209 Yes CUL4B NM_003588 X(-) 215997_s_at -1.70 1807 CXADR NM_001338 21(+) 203917_at -12.09 -1209 Yes CXCR7 NM_020311 2(+) 212977_at -11.90 -1856 Yes CXorf12 NM_003492 X(+) 204340_at -1.61 1515 DAB2 NM_001343 5(-) 201278_at -6.35 -1209 Yes DAB2IP NM_032552 9(+) 225020_at -1.78 180 Yes DAPK1 NM_004938 9(+) 203139_at -7.71 1553 Yes Yes DENND2C NM_198459 1(-) 230769_at -2.28 1488 DENND4C NM_017925 9(+) 226867_at -1.71 -247 ► DFNA5 NM_004403 7(-) 203695_s_at -3.00 -818 Yes DFNB31 NM_015404 9(-) 47553_at -3.16 -1041 DHRS3 NM_004753 1(-) 202481_at -5.19 734 ► DHX40 NM_024612 17(+) 218277_s_at -1.51 -1035 Yes DIP2B NM_173602 12(+) 224872_at -1.75 -1601 DLG5 NM_004747 10(-) 201681_s_at -1.58 734 DLG7 NM_014750 14(-) 202516_s_at -2.71 -336 Yes Yes DNAJB9 NM_012328 7(+) 202842_s_at -1.68 1836 Yes DNAJC1 NM_022365 10(-) 218409_s_at -2.07 -1031 DNAJC18 NM_152686 5(-) 227166_at -1.92 -1985 DOCK8 NM_203447 9(+) 232843_s_at -1.84 920 ► DSC2 NM_024422 18(-) 204751_x_at -23.85 -1264 Yes DSC3 NM_024423 18(-) 206032_at -61.03 -444 Yes DSG3 NM_001944 18(+) 205595_at -42.83 1354 Yes DTWD1 NM_020234 15(+) 236649_at -1.55 -1856 DUSP16 NM_030640 12(-) 224832_at -2.90 560 DZIP3 NM_014648 3(+) 213186_at -2.05 -336 EDN1 NM_001955 6(+) 218995_s_at -2.98 692 Yes EFNA1 NM_182685 1(+) 202023_at -7.72 1447 Yes Yes EHF NM_012153 11(+) 225645_at -1.92 -1395 ELOF1 NM_032377 19(-) 212418_at -1.62 -1089 ELOVL7 NM_024930 5(-) 227180_at -5.04 1121 Yes Yes

17 ENPP1 NM_006208 6(+) 205066_s_at -3.76 -237 Yes Yes EPB41L4A NM_022140 5(-) 228256_s_at -3.61 1602 Yes EPHA3 NM_182644 3(+) 206070_s_at -4.59 925 Yes Yes EPHB6 NM_004445 7(+) 204718_at -2.73 -674 Yes Yes EPS8L2 NM_022772 11(+) 218180_s_at -4.09 -1304 NM_001017 ERMAP 1(+) 219905_at -2.41 1085 922 ERN1 NM_152461 17(-) 227755_at -2.24 644 Yes Yes ► ETS2 NM_005239 21(+) 201328_at -3.36 -14 Yes EVA1 NM_005797 11(-) 203780_at -17.92 -408 EXPH5 NM_015065 11(-) 214734_at -6.72 612 ► F2RL1 NM_005242 5(+) 213506_at -8.50 -14 FABP4 NM_001442 8(-) 203980_at -9.69 -1213 Yes FAM84B NM_174911 8(-) 225864_at -23.30 -176 FAM8A1 NM_016255 6(+) 203420_at -1.82 1654 NM_001018 FANCD2 3(+) 242560_at -1.52 507 Yes 115 FANK1 NM_145235 10(+) 232968_at -3.30 830 FBLN5 NM_006329 14(-) 203088_at -5.26 -681 Yes Yes FCHO2 NM_138782 5(+) 228220_at -1.54 -245 FDFT1 NM_004462 8(+) 208647_at -2.15 -647 Yes FGFBP1 NM_005130 4(-) 205014_at -3.00 955 FLJ10986 NM_018291 1(+) 219718_at -1.89 -2373 FLJ20152 NM_019000 5(-) 218510_x_at -8.11 1556 Yes FLJ31951 NM_144726 5(-) 226077_at -2.54 1950 FLJ39653 NM_152684 4(+) 1553145_at -1.52 -1985 NM_001001 FLJ41603 5(+) 227717_at -2.94 1247 669 NM_001001 FLJ44796 5(-) 230757_at -3.10 -1930 704 FLRT3 NM_013281 20(-) 219250_s_at -7.06 -24 Yes FRS2 NM_006654 12(+) 226045_at -1.72 1429 FXYD3 NM_005971 19(+) 202489_s_at -51.10 -1299 Yes FYN NM_002037 6(-) 210105_s_at -1.59 692 Yes FZD6 NM_003506 8(+) 203987_at -2.28 -751 Yes GAB2 NM_012296 11(-) 203853_s_at -1.50 1981 Yes Yes GADD45A NM_001924 1(+) 203725_at -1.64 1354 Yes NM_001037 GALC 14(-) 204417_at -1.60 -550 525 GALNT3 NM_004482 2(-) 203397_s_at -52.52 -513 Yes Yes GALNT6 NM_007210 12(-) 219956_at -2.26 1265 Yes GATA3 NM_002051 10(+) 209602_s_at -6.09 -1786 Yes Yes GDA NM_004293 9(+) 224209_s_at -9.89 867 Yes GGH NM_003878 8(-) 203560_at -2.45 659 Yes GHR NM_000163 5(+) 205498_at -1.86 -392 Yes Yes GJA5 NM_005266 1(-) 226701_at -7.23 -14 NM_001005 GJB3 1(+) 205490_x_at -3.83 1425 752 GLI2 NM_005270 2(+) 228537_at -1.75 -1554 Yes GLMN NM_053274 1(-) 209955_s_at -2.28 -764 Yes GLUL NM_002065 1(-) 215001_s_at -1.59 -1696 Yes GLYAT NM_201648 11(-) 201432_at -1.64 -893 GM2A NM_000405 5(+) 235678_at -2.72 853

18 GM2A NM_000405 5(+) 212737_at -2.41 1070 ► GNAI1 NM_002069 7(+) 209576_at -2.98 -1696 Yes GPR1 NM_005279 2(-) 214605_x_at -2.13 -1554 GPR115 NM_153838 6(+) 1553031_at -2.15 -439 GPR126 NM_198569 6(+) 213094_at -1.76 1535 Yes Yes GPR137B NM_003272 1(+) 204137_at -1.53 -1158 ► GPRC5C NM_018653 17(+) 219327_s_at -1.84 1941 Yes Yes GPSN2 NM_138501 19(+) 208336_s_at -1.82 521 GRAMD3 NM_023927 5(+) 238049_at -5.27 -457 GRHL2 NM_024915 8(+) 219388_at -7.16 1121 GSTO2 NM_183239 10(+) 227163_at -1.84 -1161 GTF2I NM_033001 7(+) 201065_s_at -1.74 -1433 H2AFJ NM_177925 12(+) 225245_x_at -1.62 -189 HBP1 NM_012257 7(+) 209102_s_at -3.82 -560 Yes HELZ NM_014877 17(-) 203674_at -2.45 1571 HIBADH NM_152740 7(-) 231955_s_at -1.73 -1400 Yes HINT3 NM_138571 6(+) 226537_at -1.92 -192 HMGCR NM_000859 5(+) 202540_s_at -3.78 -311 Yes HMGCS1 NM_002130 5(-) 221750_at -2.15 -420 HOMER2 NM_199332 15(-) 201940_at -1.70 -109 HOOK1 NM_015888 1(+) 225792_at -18.59 1191 ► HOXA5 NM_019102 7(-) 213844_at -1.51 902 Yes Yes ► HOXA9 NM_152739 7(-) 214651_s_at -1.66 104 Yes Yes HR NM_005144 8(-) 241355_at -2.66 -63 Yes Yes HSPC159 NM_014181 2(+) 226188_at -2.34 26 ID2 NM_002166 2(+) 201566_x_at -2.55 1415 Yes Yes IGBP1 NM_001551 X(+) 202105_at -1.84 842 IGFBP2 NM_000597 2(+) 202718_at -5.07 -44 Yes NM_001013 IGFBP3 7(-) 212143_s_at -2.51 -276 Yes Yes 398 IGFL1 NM_198541 19(+) 239430_at -10.76 1488 IGSF3 NM_001542 1(-) 202421_at -2.06 -1745 Yes IL15 NM_000585 4(+) 205992_s_at -1.98 -624 Yes IL1RN NM_173843 2(+) 212657_s_at -7.06 -1507 Yes ► IL6R NM_181359 1(+) 226333_at -2.70 828 Yes IL7R NM_002185 5(+) 205798_at -2.89 673 Yes IMPA2 NM_014214 18(+) 203126_at -2.71 536 ING4 NM_016162 12(-) 218234_at -1.62 -1489 Yes INHBA NM_002192 7(-) 210511_s_at -3.51 -193 Yes Yes IRF6 NM_006147 1(-) 1552477_a_at -33.31 1718 IRX1 NM_024337 5(+) 230472_at -4.03 1388 Yes ITGB6 NM_000888 2(-) 208083_s_at -20.70 614 Yes ITGB8 NM_002214 7(+) 226189_at -3.87 699 Yes JAG1 NM_000214 20(-) 209099_x_at -2.97 -1067 Yes Yes JAK2 NM_004972 9(+) 205842_s_at -1.55 1848 Yes Yes JARID1B NM_006618 1(-) 201549_x_at -2.12 269 JMY NM_152405 5(+) 226352_at -2.23 -1018 JUB NM_032876 14(-) 225806_at -2.82 -575 Yes KCNB1 NM_004975 20(-) 211006_s_at -1.67 1848 Yes KCNK1 NM_002245 1(+) 204679_at -5.23 699 Yes KCNMB4 NM_014505 12(+) 222857_s_at -2.10 -1964 Yes

19 KIAA0319 NM_014809 6(-) 207147_at -6.73 -911 KIAA0430 NM_014647 16(-) 202386_s_at -1.56 1547 KIAA0746 NM_015187 4(-) 212314_at -2.81 1365 Yes KIAA1128 NM_018999 10(+) 209379_s_at -1.51 -1014 KIAA1166 NM_018684 X(-) 220040_x_at -1.89 -1014 KIAA1217 NM_019590 10(+) 231807_at -8.32 -786 Yes KIAA1333 NM_017769 14(+) 223257_at -1.79 -1689 KIAA1344 NM_020784 14(-) 226747_at -2.95 -1210 KIAA1370 NM_019600 15(-) 225327_at -2.61 -786 Yes KIAA1411 NM_020819 6(+) 223497_at -2.32 -572 KIAA1432 NM_020829 9(+) 226221_at -1.54 1349 ► KIAA1598 NM_018330 10(-) 221802_s_at -2.46 -373 KIAA1815 NM_024896 9(-) 218342_s_at -1.98 1090 KIAA1946 NM_177454 2(+) 227370_at -4.09 -189 NM_001017 KIAA2026 9(-) 228446_at -1.60 -1908 969 KIF14 NM_014875 1(-) 236641_at -2.09 -1843 KIF20A NM_005733 5(+) 218755_at -2.88 -431 Yes ► KLF5 NM_001730 13(+) 209211_at -1.55 -134 Yes KLK5 NM_012427 19(-) 222242_s_at -3.15 1173 Yes KRT14 NM_000526 17(-) 209351_at -26.00 -1124 Yes KRT16 NM_005557 17(-) 209800_at -44.74 1450 Yes KRT5 NM_000424 12(-) 201820_at -4.88 410 Yes KRT6A NM_005554 12(-) 214580_x_at -2.00 1558 Yes L1CAM NM_024003 X(-) 204584_at -2.13 -334 Yes Yes LAD1 NM_005558 1(-) 203287_at -3.07 598 Yes LAMA4 NM_002290 6(-) 203726_s_at -28.03 1468 Yes LAMA5 NM_005560 20(-) 210150_s_at -2.13 -1592 Yes ► LAMB1 NM_002291 7(-) 201505_at -1.97 -485 Yes LANCL1 NM_006055 2(-) 202020_s_at -1.89 -1497 ► LARP6 NM_197958 15(-) 218651_s_at -1.59 867 Yes LEPREL1 NM_018192 3(-) 218717_s_at -19.98 518 Yes LGR4 NM_018490 11(-) 218326_s_at -3.00 1899 Yes LIMA1 NM_016357 12(-) 217892_s_at -5.29 -548 ► LIMK2 NM_016733 22(+) 210582_s_at -2.99 -1305 LMBRD1 NM_018368 6(-) 218191_s_at -1.74 -1383 Yes Yes LMCD1 NM_014583 3(+) 218574_s_at -1.75 -991 LMO4 NM_006769 1(+) 209205_s_at -1.76 989 Yes LOC153222 NM_153607 5(+) 225956_at -3.22 937 ► LOX NM_002317 5(-) 204298_s_at -2.15 -485 Yes Yes LOXL1 NM_005576 15(+) 203570_at -24.64 1800 Yes Yes ► LPHN2 NM_012302 1(+) 206953_s_at -3.88 1836 LRRC16 NM_017640 6(+) 219573_at -2.34 -1751 LRRFIP2 NM_017724 3(-) 218364_at -1.55 -1751 LSR NM_015925 19(+) 208190_s_at -14.78 1294 Yes LTA4H NM_000895 12(-) 208771_s_at -1.58 795 LZTFL1 NM_020347 3(-) 218437_s_at -1.60 -1856 ► MAF NM_005360 16(-) 209348_s_at -3.94 1814 Yes Yes MAL2 NM_052886 8(+) 224650_at -24.41 722 Yes ► MAOA NM_000240 X(+) 204388_s_at -4.55 1584 Yes MAP1B NM_005909 5(+) 212233_at -6.30 -11

20 ► MAP7 NM_003980 6(-) 202890_at -8.68 -1024 MARCKS NM_002356 6(+) 225897_at -2.24 -1023 Yes Yes MARK4 NM_031417 19(+) 55065_at -1.58 1664 MBD5 NM_018328 2(+) 227839_at -2.06 -2373 MBNL1 NM_207297 3(+) 1558111_at -1.57 549 Yes MBNL2 NM_144778 13(+) 203640_at -3.16 1360 Yes MED12 NM_005120 X(+) 216071_x_at -1.53 1210 MEF2A NM_005587 15(+) 212535_at -1.55 -812 Yes MEST NM_177525 7(+) 202016_at -2.50 -189 Yes Yes MFAP3L NM_021647 4(-) 205442_at -1.80 -1429 Yes MFAP5 NM_003480 12(-) 209758_s_at -10.27 1518 Yes MGC39900 NM_194324 X(+) 214051_at -1.56 -1150 Yes MGST1 NM_145791 12(+) 239001_at -1.50 458 Yes MID2 NM_052817 X(+) 203636_at -3.67 -75 Yes MITF NM_198178 3(+) 207233_s_at -2.29 1594 Yes MKL1 NM_020831 22(-) 212748_at -2.56 876 Yes MOBKL2B NM_024761 9(-) 226844_at -3.99 683 MYLK NM_053029 3(-) 224823_at -2.10 -764 MYO18A NM_203318 17(-) 202039_at -1.58 1761 MYPN NM_032578 10(+) 235367_at -1.64 -597 NCAPD2 NM_014865 12(+) 201774_s_at -1.74 -911 NCOA7 NM_181782 6(+) 225344_at -2.12 324 Yes NDFIP2 NM_019080 13(+) 224801_at -2.16 -1568 ► NEDD4L NM_015277 18(+) 212448_at -2.20 154 NEDD9 NM_006403 6(-) 202149_at -2.31 -681 Yes NFIB NM_005596 9(-) 209289_at -3.31 339 Yes NFKBIZ NM_031419 3(+) 223218_s_at -1.78 -1121 NFYB NM_006166 12(-) 218127_at -4.43 -1169 NR1D2 NM_005126 3(+) 225768_at -2.09 955 Yes NM_001018 NR3C1 5(-) 216321_s_at -1.58 507 Yes 077 NRCAM NM_005010 7(-) 204105_s_at -5.62 1848 Yes Yes NRXN3 NM_138970 14(+) 229649_at -15.04 -245 Yes NTN4 NM_021229 12(-) 223315_at -1.98 -1880 Yes NM_001042 NUPR1 16(-) 209230_s_at -2.50 -393 Yes 483 ODF2L NM_020729 1(-) 230926_s_at -1.54 867 OIP5 NM_007280 15(-) 213599_at -1.55 -1574 OLFML2A NM_182487 9(+) 213075_at -1.70 925 Yes OLFML3 NM_020190 1(+) 218162_at -4.07 -917 Yes ORMDL1 NM_016467 2(-) 228801_at -1.86 -854 OVOL2 NM_021220 20(-) 211778_s_at -13.49 -1880 PALLD NM_016081 4(+) 200907_s_at -2.11 -1361 Yes PAN3 NM_175854 13(+) 225563_at -1.63 -189 ► PAWR NM_002583 12(-) 204005_s_at -2.60 389 Yes PCDH9 NM_203487 13(-) 219738_s_at -2.79 920 PDE4DIP NM_022359 1(-) 205872_x_at -1.84 1602 Yes PDZD2 NM_178140 5(+) 209493_at -2.39 -189 PELO NM_015946 5(+) 226731_at -3.16 762 PEX1 NM_000466 7(-) 215023_s_at -1.56 410 PHF20 NM_016436 20(+) 209422_at -1.83 -668

21 PHLDB2 NM_145753 3(+) 1557578_at -3.34 1010 Yes PHTF2 NM_020432 7(+) 209780_at -1.58 1369 PIAS1 NM_016166 15(+) 217863_at -2.16 -1232 PIK3C2B NM_002646 1(-) 204484_at -3.58 -941 ► PIR NM_003662 X(-) 207469_s_at -3.00 -745 Yes PLCE1 NM_016341 10(+) 205111_s_at -2.08 -1237 Yes Yes ► PLEKHA1 NM_021622 10(+) 219024_at -1.73 914 ► PLEKHA5 NM_019012 12(+) 220952_s_at -2.16 1556 PLEKHA6 NM_014935 1(-) 229245_at -2.64 -427 PLEKHF2 NM_024613 8(+) 218640_s_at -1.76 1470 PLEKHG3 NM_015549 14(+) 212823_s_at -1.82 1344 Yes NM_001011 PNLIPRP3 10(+) 1558846_at -27.18 -276 709 PPARA NM_005036 22(+) 226978_at -1.58 1848 Yes Yes PPL NM_002705 16(-) 203407_at -10.17 -941 Yes Yes PPP1R14C NM_030949 6(+) 226907_at -18.41 1664 Yes PPP2R2B NM_181678 5(-) 213849_s_at -5.88 -974 Yes PRDM2 NM_015866 1(+) 205277_at -1.88 1191 Yes PRICKLE2 NM_198859 3(-) 225968_at -1.97 -1615 PRKAB2 NM_005399 1(-) 1558027_s_at -2.19 -917 PRKCH NM_006255 14(+) 218764_at -2.34 -237 Yes Yes PRKCI NM_002740 3(+) 213518_at -1.51 446 Yes ► PROS1 NM_000313 3(-) 207808_s_at -1.97 1946 PTGFRN NM_020440 1(+) 224950_at -2.01 1369 PTPLB NM_198402 3(-) 227741_at -2.93 1916 PTPRK NM_002844 6(-) 203038_at -1.64 446 R3HDM2 NM_014925 12(-) 203831_at -1.75 -671 RAB25 NM_020387 1(+) 218186_at -16.14 1054 RAB2B NM_032846 14(-) 225074_at -1.53 176 RAB9A NM_004251 X(+) 221808_at -1.87 220 Yes RABGAP1 NM_012197 9(+) 213313_at -1.80 1471 RALGPS2 NM_152663 1(+) 227224_at -2.75 1475 RB1CC1 NM_014781 8(-) 202033_s_at -1.79 -1565 Yes NM_001034 RBM35A 8(+) 225846_at -72.00 -1161 915 RECK NM_021111 9(+) 205407_at -1.80 -590 Yes RGC32 NM_014059 13(+) 218723_s_at -8.22 1311 Yes NM_001005 RGS10 10(-) 204319_s_at -1.68 -578 Yes 339 ► RGS12 NM_198227 4(+) 205823_at -1.74 1916 Yes RHOBTB3 NM_014899 5(+) 202975_s_at -2.38 -513 RHOF NM_019034 12(-) 219045_at -2.11 1135 RIPK4 NM_020639 21(-) 221215_s_at -11.41 -808 Yes RND3 NM_005168 2(-) 212724_at -2.49 654 RNF103 NM_005667 2(-) 202636_at -1.58 1782 Yes RNF12 NM_183353 X(-) 242121_at -1.93 174 RNF141 NM_016422 11(-) 226106_at -1.64 -440 RNF150 NM_020724 4(-) 227657_at -6.26 867 Yes RNF36 NM_182985 15(+) 1568592_at -1.71 -1161 RP6- NM_001042 X(+) 218499_at -1.95 -459 213H19.1 452 S100A2 NM_005978 1(-) 204268_at -2.70 -853 Yes

22 S100A8 NM_002964 1(-) 202917_s_at -3.62 -1256 Yes SC5DL NM_006918 11(+) 211423_s_at -1.57 639 SCARA3 NM_016240 8(+) 219416_at -1.57 1654 Yes SCARB1 NM_005505 12(-) 201819_at -1.88 -971 SCEL NM_003843 13(+) 206884_s_at -25.56 1050 SCHIP1 NM_014575 3(+) 204030_s_at -1.86 -991 SDCBP2 NM_080489 20(-) 233565_s_at -2.14 1436 SDK1 NM_152744 7(+) 229407_at -1.59 -143 Yes SEPTIN6 NM_145799 X(-) 1555526_a_at -2.79 1399 SERPINB1 NM_012397 18(+) 217272_s_at -12.84 1173 3 SETBP1 NM_015559 18(+) 205933_at -2.54 491 ► SFRP1 NM_003012 8(-) 202037_s_at -4.05 573 Yes Yes SGPP2 NM_152386 2(+) 244780_at -7.42 910 Yes SGTB NM_019072 5(-) 228745_at -1.57 -662 SH3PXD2A NM_014631 10(-) 224817_at -2.53 -146 SH3YL1 NM_015677 2(-) 204019_s_at -1.63 1204 SLC12A6 NM_005135 15(-) 226741_at -1.52 955 Yes SLC16A5 NM_004695 17(+) 206600_s_at -1.54 -1875 Yes Yes SLC1A3 NM_004172 5(+) 202800_at -1.67 -999 Yes SLC29A3 NM_018344 10(+) 219344_at -3.19 -96 SLC7A8 NM_012244 14(-) 216092_s_at -4.58 -598 Yes Yes SLPI NM_003064 20(-) 203021_at -3.80 -1158 Yes ► SMARCA1 NM_139035 X(-) 203874_s_at -1.94 1685 SMCR7 NM_139162 17(+) 235896_s_at -1.81 585 SNX13 NM_015132 7(-) 1553148_a_at -1.97 874 SNX16 NM_152837 8(-) 229618_at -1.79 -345 SORBS2 NM_003603 4(-) 204288_s_at -1.79 -821 Yes SORT1 NM_002959 1(-) 212807_s_at -2.49 446 Yes Yes SOS2 NM_006939 14(-) 212870_at -1.91 1619 SPINT1 NM_181642 15(+) 202826_at -7.11 -97 Yes SPINT2 NM_021102 19(+) 210715_s_at -41.48 -590 Yes SPRR1B NM_003125 1(+) 205064_at -206.81 -1158 ST14 NM_021978 11(+) 202005_at -3.26 1637 Yes Yes ST6GALNA NM_006456 17(-) 204542_at -2.61 -74 Yes C2 ST6GALNA NM_152996 1(+) 235334_at -1.70 -421 C3 STAT3 NM_213662 17(-) 208991_at -1.66 832 Yes STAU2 NM_014393 8(-) 227179_at -1.61 -641 Yes Yes STX7 NM_003569 6(-) 212632_at -2.11 -751 ► SYNE2 NM_182910 14(+) 202761_s_at -3.03 -272 SYNPO NM_007286 5(+) 202796_at -1.74 -1511 TACSTD1 NM_002354 2(+) 201839_s_at -7.17 -1023 Yes TANC1 NM_033394 2(+) 225308_s_at -1.73 1086 TES NM_152829 7(+) 202720_at -1.62 -143 Yes NM_001042 TFAP2A 6(-) 204653_at -2.00 -920 Yes 425 TFCP2L1 NM_014553 2(-) 227642_at -2.12 1561 TGFB1I1 NM_015927 16(+) 209651_at -1.57 1294 TLE1 NM_005077 9(-) 203221_at -1.81 1848 ► TLE4 NM_007005 9(+) 204872_at -2.23 -925

23 TLN2 NM_015059 15(+) 212701_at -2.78 -1391 TM4SF1 NM_014220 3(-) 209386_at -1.87 1238 Yes TMEM166 NM_032181 2(-) 227828_s_at -2.26 -1876 TMEM40 NM_018306 3(-) 222892_s_at -9.17 -2373 TMEM63C NM_020431 14(+) 227733_at -2.19 1369 NM_001008 TMEM64 8(-) 225974_at -1.84 -1550 495 TMEM77 NM_178454 1(-) 225230_at -1.59 -563 TMEM98 NM_015544 17(+) 223170_at -2.23 972 ► TNFAIP8 NM_014350 5(+) 208296_x_at -2.25 -430 TNFRSF21 NM_014452 6(-) 214581_x_at -2.22 695 Yes TNS3 NM_022748 7(-) 217853_at -1.96 1376 TOM1L1 NM_005486 17(+) 204485_s_at -1.51 957 Yes TP53INP1 NM_033285 8(-) 225912_at -2.92 -1135 Yes TP53INP2 NM_021202 20(+) 224836_at -2.35 -1880 TPD52L1 NM_003287 6(+) 210372_s_at -10.10 758 Yes NM_001018 TPM1 15(+) 238688_at -2.80 686 Yes Yes 020 TPX2 NM_012112 20(+) 210052_s_at -1.62 1143 TRIM22 NM_006074 11(+) 213293_s_at -2.21 -532 TRIM29 NM_012101 11(-) 202504_at -8.67 1941 Yes TSC22D3 NM_198057 X(-) 208763_s_at -2.22 1018 Yes Yes TSPAN1 NM_005727 1(+) 209114_at -1.94 1782 TSPAN13 NM_014399 7(+) 217979_at -2.39 1430 TSPAN14 NM_030927 10(+) 223314_at -1.60 940 TTK NM_003318 6(+) 204822_at -1.66 758 Yes Yes TXNRD1 NM_182743 12(+) 201266_at -1.70 -272 UGT1A4 NM_007120 2(+) 204532_x_at -3.19 78 UNC5B NM_170744 10(+) 226899_at -5.13 -27 Yes USP53 NM_019050 4(+) 230083_at -1.90 -651 Yes VAMP8 NM_003761 2(+) 202546_at -1.67 1029 WDR44 NM_019045 X(+) 219297_at -1.59 -651 WWC1 NM_015238 5(+) 213085_s_at -1.98 -1932 WWOX NM_130844 16(+) 219077_s_at -1.70 1840 Yes NM_001005 YPEL2 17(+) 227020_at -3.80 -828 Yes 404 YTHDC1 NM_133370 4(-) 212455_at -1.53 -1046 ZBTB20 NM_015642 3(-) 205383_s_at -2.05 -714 Yes ZBTB41 NM_194314 1(-) 226962_at -2.02 1932 ZBTB44 NM_014155 11(-) 225845_at -1.93 1873 ZCCHC11 NM_015269 1(-) 212704_at -1.71 1395 ZCCHC6 NM_024617 9(-) 220933_s_at -1.73 -1948 ZDHHC4 NM_018106 7(+) 220261_s_at -18.28 -247 ZFHX1B NM_014795 2(-) 235593_at -3.17 1252 Yes Yes ZFYVE1 NM_021260 14(-) 223387_at -1.80 1363 ZHX2 NM_014943 8(+) 203556_at -1.98 1361 Yes ZNF185 NM_007150 X(+) 203585_at -1.72 78 Yes ZNF33B NM_006955 10(-) 215022_x_at -1.97 1504 ZNF419A NM_024691 19(+) 219826_at -1.51 -266 ZNF488 NM_153034 10(+) 229901_at -2.21 1211 ZNF532 NM_018181 18(+) 220617_s_at -1.59 -806

24 ZNF548 NM_152909 19(+) 1553719_s_at -1.60 -1493 ZNF608 NM_020747 5(-) 229817_at -2.55 -134 ZNF618 NM_133374 9(+) 226590_at -1.80 -1136 ZNF638 NM_014497 2(+) 239243_at -2.08 1453 ZRANB1 NM_017580 10(+) 225131_at -2.65 -1176 ZSCAN2 NM_181877 15(+) 231188_at -1.59 -1255 ZUBR1 NM_020765 1(-) 211950_at -1.58 305 Note: a) 488 genes, showed in Figure 1D, were listed by following alphabetical order in table. Gene symbols in bold are 325 genes that were subjected to in silico gene expression analysis shown in Figure 2A. The arrow heads indicate 40 genes selected for validation experiments. b) Chr. stands for chromosome number. c) The down-regulated gene expressions were analyzed by comparison of AKT1 and vector transfected MCF10A samples. The cut-off value was set as 1.5 fold. d) ChIP-Seq of H3K27me3 revealed enrichment peak most close to 5′ TSS region of each gene. e) 113 loci were also reported as polycomb-targeted genes in human and mouse embryonic stem cells (Boyer et al., 2006; Lee et al., 2006; Both references cited in main text). f) 172 genes were shown to associate with cancer by functional analysis conducted by IPA (Ingenuity Pathway Analysis) software.

25 Table S4. Genes (n=1005) enriched with H3K27me3 but without downregulation H3K27me3 Gene peak Cancer b Accession Chr. Strand a Function Symbol (distance to Related TSS [bp]) AASS NM_005763 7 - 1711 ABCB11 NM_003742 2 - 378 ABCB4 NM_018850 7 - 1986 ABCB5 NM_178559 7 + 532 ACF NM_138933 10 - 240 ACOT9 NM_001037171 X - -1373 ACVR1C NM_145259 2 - -861 ADAM2 NM_001464 8 - 1335 ADAM22 NM_021723 7 + -536 ADAM23 NM_003812 2 + 1989 ADAM28 NM_021777 8 + 1877 ADAM30 NM_021794 1 - -865 ADAM7 NM_003817 8 + -782 ADAMTSL1 NM_052866 9 + -2165 ADARB1 NM_015834 21 + 859 ADORA1 NM_000674 1 + 1497 ADRA1B NM_000679 5 + -616 ADRA2A NM_000681 10 + -1709 ADRA2C NM_000683 4 + -992 AFF3 NM_002285 2 - 1068 AFM NM_001133 4 + 176 AFP NM_001134 4 + -495 AGC1 NM_013227 15 + -992 AGTR2 NM_000686 X + -1029 AGXT2L1 NM_031279 4 - 1657 AKAP3 NM_006422 12 - 1603 ALB NM_000477 4 + -968 ALDH1A1 NM_000689 9 - 1688 ALDOB NM_000035 9 - 775 ALK NM_004304 2 - -1165 ALLC NM_199232 2 + 816 ALOX5 NM_000698 10 + -933 AMICA1 NM_153206 11 - 817 AMMECR1 NM_015365 X - -965 ANKRD19 NM_001010925 9 + 531 ANKRD43 NM_175873 5 + -230 ANKRD56 NM_001029870 4 - -975 ANKRD6 NM_014942 6 + -149 ANKRD7 NM_019644 7 + 907 AP1S2 NM_003916 X - 1220 APBA1 NM_001163 9 - -1859 APBB1IP NM_019043 10 + -1570 ARHGAP25 NM_001007231 2 + -570 ARHGAP26 NM_015071 5 + 1126 ARMC2 NM_032131 6 + 1084 ARMC4 NM_018076 10 - 1082 ARR3 NM_004312 X + 75 ARSF NM_004042 X + 1849 ART1 NM_004314 11 + 1365

26 ASAH2 NM_019893 10 - -582 ASB11 NM_080873 X - -1453 ASCL4 NM_203436 12 + -590 ASRGL1 NM_025080 11 + -639 ATOH1 NM_005172 4 + -2899 ATP11C NM_173694 X - 212 ATP13A4 NM_032279 3 - -711 ATP13A5 NM_198505 3 - -493 ATP2B2 NM_001683 3 - -1055 ATP6AP2 NM_005765 X + -1858 ATP6V1C2 NM_144583 2 + -1124 ATRNL1 NM_207303 10 + -912 B3GALT1 NM_020981 2 + -1526 BARX2 NM_003658 11 + 1457 BCL9 NM_004326 1 + -504 BET1 NM_005868 7 - -1775 BHMT2 NM_017614 5 + 663 BMP6 NM_001718 6 + -1307 Yes Growth factor BMPR1B NM_001203 4 + -4349 BMX NM_203281 X + 1329 BOC NM_033254 3 + 1737 BPIL3 NM_174897 20 + -713 BRS3 NM_001727 X + 1511 BSPRY NM_017688 9 + -1064 BTBD11 NM_001018072 12 + -1825 BTNL2 NM_019602 6 - 377 BTNL3 NM_197975 5 + 1895 BTNL9 NM_152547 5 + 645 C10orf107 NM_173554 10 + -1523 C10orf11 NM_032024 10 + -1523 C10orf92 NM_017609 10 - 325 C11orf40 NM_144663 11 - -1675 C11orf53 NM_198498 11 + -615 C13orf18 NM_025113 13 - 1084 C14orf105 NM_018168 14 - 878 C14orf37 NM_001001872 14 - 999 C14orf39 NM_174978 14 - -299 C16orf78 NM_144602 16 + 193 C18orf26 NM_173629 18 + -986 C1orf120 NM_001010899 1 + -177 C1orf126 NM_182534 1 - 846 C1orf158 NM_152290 1 + -1548 C1orf173 NM_001002912 1 - 509 C1orf24 NM_052966 1 - 1504 C1orf32 NM_199351 1 - -916 C1orf76 NM_173509 1 + -919 C1orf87 NM_152377 1 - -587 C1orf95 NM_001003665 1 + 678 C1QB NM_000491 1 + 1733 C20orf186 NM_182519 20 + -1914 C21orf34 NM_001005732 21 + -311 C22orf30 NM_173566 22 - -1970 C3orf52 NM_024616 3 + 1973 C3orf57 NM_001040100 3 - 136

27 C4BPA NM_000715 1 + 1272 C4orf26 NM_178497 4 + 120 C4orf7 NM_152997 4 + -1202 C5orf23 NM_024563 5 + -500 C5orf29 NM_152687 5 + -185 C6orf105 NM_032744 6 - 1051 C6orf122 NM_207502 6 - 1045 C6orf174 NM_001012279 6 - 561 C7orf16 NM_006658 7 + 730 C7orf9 NM_022150 7 - -471 C8A NM_000562 1 + 835 C8orf22 NM_001007176 8 + 1442 C9orf19 NM_022343 9 + 460 C9orf66 NM_152569 9 - -960 CA5B NM_007220 X + -931 CABP5 NM_019855 19 - -1285 CACNB2 NM_201590 10 + 1092 CACNB4 NM_000726 2 - -511 CACNG2 NM_006078 22 - 1548 CACYBP NM_001007214 1 + -1092 CADPS NM_183394 3 - -1307 CALN1 NM_031468 7 - 1538 CAMKK2 NM_172215 12 - -1807 CAPN13 NM_144575 2 - -886 CAPN6 NM_014289 X - -1094 CAPSL NM_144647 5 - 1637 CCL15 NM_032965 17 - -1976 CCR2 NM_000648 3 + -1442 CCR3 NM_178329 3 + -190 CCR5 NM_000579 3 + -635 CCR9 NM_031200 3 + -921 CD1B NM_001764 1 - -619 CD302 NM_014880 2 - -1402 CD36 NM_001001547 7 + -57 CD3G NM_000073 11 + 891 CD40LG NM_000074 X + 0 CD5L NM_005894 1 - -1326 CD69 NM_001781 12 - 437 CD84 NM_003874 1 - 1286 CDH26 NM_021810 20 + 178 CDS NM_001263 4 + 1021 CEACAM21 NM_033543 19 + -1125 CEACAM3 NM_001815 19 + 206 CEP192 NM_032142 18 + 503 CFTR NM_000492 7 + 949 CHGB NM_001819 20 + -1866 CHIT1 NM_003465 1 - 1598 CHRDL1 NM_145234 X - -1852 CHRM2 NM_001006630 7 + -1537 CHRNA6 NM_004198 8 - 575 CHST13 NM_152889 3 + -264 CHST9 NM_031422 18 - 1976 CHX10 NM_182894 14 + 1874 CLCA1 NM_001285 1 + -337

28 CLCN4 NM_001830 X + 665 CLCN5 NM_000084 X + 1106 CLDN10 NM_006984 13 + 1641 CLDN2 NM_020384 X + 612 CLEC14A NM_175060 14 - -476 CLEC1B NM_016509 12 - 1245 CLEC2A NM_207375 12 - 588 CLEC4D NM_080387 12 + 699 CLEC5A NM_013252 7 - -1649 CLUL1 NM_014410 18 + -796 CNGA2 NM_005140 X + -772 CNTN5 NM_175566 11 + 521 CNTNAP4 NM_138994 16 + -1748 COBL NM_015198 7 - 389 COL15A1 NM_001855 9 + -609 COL4A3 NM_031366 2 + 877 COLEC10 NM_006438 8 + 175 COVA1 NM_182314 X - 1188 COX7B NM_001866 X + 785 COX7B2 NM_130902 4 - 679 CPA3 NM_001870 3 + -72 CPB1 NM_001871 3 + -76 CPLX4 NM_181654 18 - -440 CPVL NM_031311 7 - 777 CR1 NM_000651 1 + -1494 CR2 NM_001877 1 + 1009 CRLF1 NM_004750 19 - -1241 CRSP2 NM_004229 X - -1974 CRX NM_000554 19 + -909 CSMD3 NM_198124 8 - 1057 CSN1S1 NM_001025104 4 + -1086 CSN2 NM_001891 4 - 1014 CSS3 NM_175856 5 + -1120 CST9 NM_001008693 20 - 1012 CTNNA3 NM_013266 10 - -668 CTNNAL1 NM_003798 9 - 1584 CXCL10 NM_001565 4 - 373 CXCL14 NM_004887 5 - -1333 CXCR4 NM_001008540 2 - 1182 CXorf23 NM_198279 X - 1044 CXorf34 NM_024917 X - -1475 CXorf45 NM_001039210 X + 1668 CXorf48 NM_017863 X - -784 CXorf6 NM_005491 X + 224 CYFIP2 NM_014376 5 + 762 CYP11B2 NM_000498 8 - -1940 CYP2J2 NM_000775 1 - -290 CYS1 NM_001037160 2 - -812 DACH1 NM_080760 13 - -670 DACT1 NM_016651 14 + -410 DBX2 NM_001004329 12 - -1652 DCD NM_053283 12 - -1085 DCX NM_000555 X - 1229 DEFB104A NM_080389 8 + -101

29 DEFB110 NM_001037728 6 - 606 DEFB118 NM_054112 20 + -587 DEFB125 NM_153325 20 + 151 DEFB126 NM_030931 20 + -1050 DEFB127 NM_139074 20 + 1416 DEFB128 NM_001037732 20 - 537 DEFB129 NM_080831 20 + -1723 DEFB134 NM_001033019 8 - -1132 DEPDC2 NM_025170 8 + 1045 DGAT2L3 NM_001013579 X + -169 DGKB NM_004080 7 - 488 DIO1 NM_213593 1 + -1047 DIRAS2 NM_017594 9 - -373 DISP1 NM_032890 1 + -1804 DLG2 NM_001364 11 - -788 DLG3 NM_021120 X + -742 DLX5 NM_005221 7 - -222 DMRT1 NM_021951 9 + 1712 DPF3 NM_012074 14 - 1861 DPYSL3 NM_001387 5 - -848 G-protein coupled DRD2 NM_016574 11 - -1710 Yes receptor DSG1 NM_001942 18 + 952 DSG4 NM_177986 18 + -136 DTNA NM_032981 18 + 772 DTWD2 NM_173666 5 - -562 DUB3 NM_201402 8 - -1723 ECOP NM_030796 7 - -1807 EDAR NM_022336 2 - 41 EDEM3 NM_025191 1 - -674 EDG7 NM_012152 1 - 471 EFEMP1 NM_001039349 2 - -465 EGFLAM NM_152403 5 + 1612 Receptor tyrosine EGFR NM_201284 7 + -1817 Yes kinase EHD3 NM_014600 2 + -1205 EIF5 NM_183004 14 + 513 ELMOD1 NM_018712 11 + -1085 ELSPBP1 NM_022142 19 + 859 EMR1 NM_001974 19 + 820 EMR3 NM_152939 19 - 1109 ENOSF1 NM_017512 18 - -1459 ENPP4 NM_014936 6 + -1969 ENTPD4 NM_004901 8 - 1080 EPHA5 NM_182472 4 - -897 EPHA7 NM_004440 6 - -808 ERC2 NM_015576 3 - 1230 ERG NM_004449 21 - -1013 EVI5 NM_005665 1 - -1252 EVX1 NM_001989 7 + 913 EYA1 NM_000503 8 - 1120 EYA4 NM_172105 6 + -986 F11 NM_019559 4 + 1030 FA2H NM_024306 16 - 321

30 FAM12B NM_022360 14 + 1176 FAM13C1 NM_001001971 10 - -543 FAM70B NM_182614 13 - 772 FAM77D NM_173688 8 + -953 FAM80A NM_173642 1 + 1333 FAM83B NM_001010872 6 + -226 FBP1 NM_000507 9 - 923 FBXL21 NM_012159 5 + -160 FCER2 NM_002002 19 - 1996 FCGBP NM_003890 19 - 1872 FCRL1 NM_052938 1 - 1686 FCRL2 NM_138738 1 - 1038 FCRL3 NM_052939 1 - -930 FCRL5 NM_031281 1 - 1333 FGF1 NM_033137 5 - -1189 FGF12 NM_004113 3 - -335 FGF13 NM_033642 X - -120 FGF20 NM_019851 8 - -356 FGF9 NM_002010 13 + 427 FKSG83 NM_032030 6 + -655 FLJ10159 NM_018013 6 + -1359 FLJ16171 NM_001004348 5 - -1961 FLJ20366 NM_017786 8 - 121 FLJ23577 NM_144722 5 + -1444 FLJ25770 NM_178555 4 - 119 FLJ32063 NM_153031 2 + 1638 FLJ32110 NM_181646 7 + -1487 FLJ37060 NM_001039903 6 + 1123 FLJ40235 NM_173635 19 + -1474 FLJ40288 NM_173682 7 + 309 FLJ42486 NM_207379 14 - -1659 FLJ42953 NM_207474 22 + 997 FLJ43390 NM_001039785 14 + -26 FLJ43763 NM_001039892 6 + 189 FLJ44881 NM_207461 18 + -572 FOXI1 NM_144769 5 + 907 FOXN4 NM_213596 12 - -1693 FOXP2 NM_148900 7 + 890 FPGT NM_003838 1 + 1588 FREM1 NM_144966 9 - 1492 FREM2 NM_207361 13 + -680 FRMD5 NM_032892 15 - 820 FRMD7 NM_194277 X - 228 FSTL4 NM_015082 5 - -1579 FSTL5 NM_020116 4 - 2465 G3BP NM_198395 5 + 1733 G6PC2 NM_021176 2 + -586 GABBR2 NM_005458 9 - -1301 GABRA4 NM_000809 4 - -1064 GABRB1 NM_000812 4 + -634 GABRP NM_014211 5 + 1059 GALNAC4S- NM_015892 10 - -970 6ST GALNT12 NM_024642 9 + -600

31 GALNT8 NM_017417 12 + 1889 GALNTL5 NM_145292 7 + -1642 GALR1 NM_001480 18 + -1419 GARNL1 NM_194301 14 - 1282 GAS2 NM_177553 11 + -1628 GCA NM_012198 2 + -194 GDAP1L1 NM_024034 20 + -320 GDF10 NM_004962 10 - -529 GDNF NM_199231 5 - 351 Yes Growth factor GFI1B NM_004188 9 + 1283 GFM1 NM_024996 3 + 691 GFRA4 NM_145762 20 - 745 GFRAL NM_207410 6 + 576 GHRH NM_021081 20 - 305 Yes Growth hormone GIMAP4 NM_018326 7 + -689 GK2 NM_033214 4 - -405 GLDN NM_181789 15 + 1597 GLRA3 NM_006529 4 - 548 GLULD1 NM_016571 6 - 1240 GML NM_002066 8 + 1283 GMPR NM_006877 6 + -688 GPC5 NM_004466 13 + 1614 GPM6A NM_201592 4 - -459 GPM6B NM_001001994 X - 1051 GPR12 NM_005288 13 - -1537 GPR133 NM_198827 12 + -988 GPR144 NM_182611 9 + -42 GPR158 NM_020752 10 + -994 GPR31 NM_005299 6 - -1092 GPR63 NM_030784 6 - 520 GPR98 NM_032119 5 + -1071 GPX2 NM_002083 14 - 583 GPX5 NM_003996 6 + 834 GPX6 NM_182701 6 - 648 GRHL1 NM_198182 2 + -543 GRHL3 NM_198173 1 + 534 GRIA4 NM_000829 11 + -733 GRID2 NM_001510 4 + -829 GRIK1 NM_000830 21 - -448 GRIP1 NM_021150 12 - -1081 GRK1 NM_002929 13 + 1304 GSTA5 NM_153699 6 - 1151 GUCY1A3 NM_000856 4 + -326 GULP1 NM_016315 2 + -1833 H3F3A NM_002107 1 + -1342 Transmembrane HAVCR2 NM_032782 5 - 415 Yes receptor HBB NM_000518 11 - -724 HBE1 NM_005330 11 - 348 HCCS NM_005333 X + 1829 HCG3 NM_001001394 2 - 899 HCK NM_002110 20 + -1716 HCRTR2 NM_001526 6 + 1672 HEMGN NM_197978 9 - 1446

32 HFM1 NM_001017975 1 - -1447 HGF NM_001010934 7 - 1887 Yes Growth factor HLA-DQA1 NM_002122 6 + 641 HLA-DQA2 NM_020056 6 + 161 HLA-DRB5 NM_002125 6 - 117 HMCN1 NM_031935 1 + -704 HMP19 NM_015980 5 + -1128 HOXD13 NM_000523 2 + 1524 HPRT1 NM_000194 X + -1421 HPSE2 NM_021828 10 - -1592 HSD3B2 NM_000198 1 + -1094 HTN3 NM_000200 4 + -1263 HTR1E NM_000865 6 + -627 HTR2A NM_000621 13 - 175 HTR3B NM_006028 11 + -797 HTR4 NM_001040174 5 - -667 HTR5A NM_024012 7 + 1123 HYDIN NM_017558 16 - -1131 IAPP NM_000415 12 + -383 ICA1 NM_004968 7 - -191 ID4 NM_001546 6 + -394 IFNA6 NM_021002 9 - -815 IFNG NM_000619 12 - 1887 Yes Cytokine IGFL4 NM_001002923 19 - 587 IGSF1 NM_205833 X - -365 IGSF10 NM_178822 3 - -14 IGSF11 NM_001015887 3 - 265 IKBKG NM_003639 X + 1846 IKZF3 NM_183232 17 - -634 IL13RA2 NM_000640 X - 1862 Transmembrane IL15RA NM_002189 10 - 1942 Yes receptor IL17D NM_138284 13 + -780 IL18 NM_001562 11 - -851 Yes Cytokine IL1F10 NM_032556 2 + 36 IL22 NM_020525 12 - -53 IL7 NM_000880 8 - 1412 INA NM_032727 10 + -1408 INTS6 NM_001039938 13 - -1225 IQGAP2 NM_006633 5 + 1897 Yes Cell signaling Transcription IRF1 NM_002198 5 - -1675 Yes regulator IRF8 NM_002163 16 + 227 ITGA8 NM_003638 10 - 175 ITGB2 NM_000211 21 - -1198 ITGBL1 NM_004791 13 + 235 ITIH1 NM_002215 3 + 1654 ITK NM_005546 5 + 117 KATNA1 NM_007044 6 - 220 KCNA5 NM_002234 12 + -1644 KCND3 NM_172198 1 - 99 KCNIP1 NM_001034838 5 + -1057 KCNIP4 NM_147183 4 - 726 KCNJ2 NM_000891 17 + -969

33 KCNJ3 NM_002239 2 + 1963 KCNJ9 NM_004983 1 + 718 KCNMB1 NM_004137 5 - 1115 KCNMB2 NM_005832 3 + -210 KCNQ5 NM_019842 6 + 1946 KIAA0523 NM_015253 17 + -1956 KIAA0672 NM_014859 17 + -1179 KIAA0703 NM_014861 16 + -1432 KIAA0774 NM_001033602 13 + -46 KIAA0789 NM_014653 12 + -1339 KIAA1576 NM_020927 16 + 1818 KIAA1900 NM_052904 6 + -924 KIAA1900 NM_052904 6 + -24 KIAA1913 NM_052913 6 + -253 KLHL13 NM_033495 X - -1920 KLHL3 NM_017415 5 - -639 KLK3 NM_001648 19 + -1581 KLRD1 NM_002262 12 + -482 KRT2 NM_000423 12 - -1975 KRT20 NM_019010 17 - -1696 KRT222P NM_152349 17 - -711 KRT26 NM_181539 17 - -1364 KRT28 NM_181535 17 - -291 KRT39 NM_213656 17 - 431 KRT72 NM_080747 12 - 158 KRT76 NM_015848 12 - -1629 KRT9 NM_000226 17 - 1735 KRTAP13-1 NM_181599 21 + -1761 KRTAP13-3 NM_181622 21 - -200 KRTAP13-4 NM_181600 21 + -863 KRTAP1-5 NM_031957 17 - -1921 KRTAP15-1 NM_181623 21 + -1615 KRTAP3-1 NM_031958 17 - -209 KRTAP8-1 NM_175857 21 - 460 KSR1 NM_014238 17 + -1861 Yes Kinase LAIR1 NM_021706 19 - -1568 LBH NM_030915 2 + 1401 LBR NM_194442 1 - -1059 LCE1A NM_178348 1 + -671 LCP1 NM_002298 13 - 1706 LEMD1 NM_001001552 1 - 197 LGALS13 NM_013268 19 + -107 LGALS14 NM_203471 19 + -484 LGI2 NM_018176 4 - 1512 LGR5 NM_003667 12 + -478 LHFPL3 NM_199000 7 + -738 LHX4 NM_033343 1 + -1163 LILRA1 NM_006863 19 + -1823 LILRA2 NM_006866 19 + -269 LILRA4 NM_012276 19 - 632 LILRB1 NM_006669 19 + -739 LILRB4 NM_006847 19 + -1862 LIN28B NM_001004317 6 + -414 LIN7A NM_004664 12 - -276

34 LIPG NM_006033 18 + -1023 LIPI NM_198996 21 - -876 LOC153328 NM_145282 5 + 1238 LOC196541 NM_001010977 13 - -346 LOC283514 NM_198849 13 - 543 LOC283677 NM_001042367 15 + -1650 LOC285735 NM_001037231 6 + -410 LOC375449 NM_198828 5 + -262 LOC388882 NM_001006606 22 - 566 LOC389936 NM_001013656 10 + 1472 LOC401498 NM_212558 9 + 1505 LOC440993 NM_001013714 3 + -100 LOC63920 NM_022090 5 - 637 LOC643923 NM_001039772 11 + 1221 LOC92196 NM_001017920 2 + -985 LONRF2 NM_198461 2 - -602 LOXHD1 NM_144612 18 - -877 LPL NM_000237 8 + -856 LPO NM_006151 17 + -245 LPPR4 NM_014839 1 + 914 LRAT NM_004744 4 + 1989 LRCH2 NM_020871 X - -110 LRP1B NM_018557 2 - -1961 LRRC18 NM_001006939 10 - -818 LRRC7 NM_020794 1 + -1244 LRRC8C NM_032270 1 + 1752 LSM6 NM_007080 4 + -1941 LUM NM_002345 12 - -1228 LYPD5 NM_182573 19 - -375 LYSMD2 NM_153374 15 - -993 LYSMD3 NM_198273 5 - -1444 MAP3K14 NM_003954 17 - -578 Yes Kinase MAPK4 NM_002747 18 + 220 MARCO NM_006770 2 + 587 MARK1 NM_018650 1 + 1711 MBIP NM_016586 14 - -605 MBNL3 NM_018388 X - 102 MBTPS2 NM_015884 X + -1173 MC4R NM_005912 18 - 339 MCF2 NM_005369 X - -1883 MCTP1 NM_024717 5 - 1134 MDS1 NM_004991 3 - -1133 MED12L NM_053002 3 + 736 MEF2C NM_002397 5 - 821 MEGF10 NM_032446 5 + -812 MEIS3 NM_020160 19 - -1804 MEOX2 NM_005924 7 - 1632 MEP1B NM_005925 18 + 1716 MGC10823 NM_182664 1 + -1100 MGC26647 NM_152706 7 - 866 MGC34821 NM_173586 11 - 232 MGC35295 NM_152717 11 + 1250 MGC45438 NM_152459 16 - -1428 MID1IP1 NM_021242 X + -1015

35 MIER3 NM_152622 5 - -1990 MIP NM_012064 12 - -205 MLSTD1 NM_018099 12 + -1063 MMP20 NM_004771 11 - 528 MMP24 NM_006690 20 + -615 MMP26 NM_021801 11 + 1102 MNDA NM_002432 1 + -90 MOGAT2 NM_025098 11 + -1880 MORC4 NM_024657 X - -272 MPPED2 NM_001584 11 - -1485 MRGPRX2 NM_054030 11 - -697 MSI1 NM_002442 12 - 1140 MSX2 NM_002449 5 + -1079 MTAC2D1 NM_152332 14 - 835 MTMR1 NM_003828 X + 1075 MTTP NM_000253 4 + 98 MTUS1 NM_001001927 8 - -935 MUC20 NM_152673 3 + -1218 MXRA5 NM_015419 X - 373 MYCL1 NM_005376 1 - 1173 MYH1 NM_005963 17 - 417 MYH2 NM_017534 17 - 401 MYH8 NM_002472 17 - 646 MYL1 NM_079420 2 - -1359 MYLIP NM_013262 6 + -694 MYOD1 NM_002478 11 + -684 MYOM2 NM_003970 8 + -53 MYOT NM_006790 5 + 1729 NAALAD2 NM_005467 11 + -428 NALP9 NM_176820 19 - -121 NAP1L2 NM_021963 X - 1608 NAV3 NM_014903 12 + -2426 NBEA NM_015678 13 + -854 NCKAP1L NM_005337 12 + 1706 NCR2 NM_004828 6 + 1397 NDST3 NM_004784 4 + 54 NDST4 NM_022569 4 - 1480 NEF3 NM_005382 8 + -1610 NEFL NM_006158 8 - -1158 NELL2 NM_006159 12 - 1504 NEUROD4 NM_021191 12 + -487 NEUROD6 NM_022728 7 - -538 NFASC NM_015090 1 + -1044 NGFB NM_002506 1 - 879 NHLRC1 NM_198586 6 - 1629 NKAP NM_024528 X - -1438 NKD1 NM_033119 16 + -1240 NLGN1 NM_014932 3 + -1036 NMNAT2 NM_015039 1 - 141 NOS2A NM_153292 17 - -1719 Yes Enzyme NOX4 NM_016931 11 - 400 NPHS2 NM_014625 1 - 790 NPS NM_001030013 10 + -301 NPY2R NM_000910 4 + -1229

36 NR3C2 NM_000901 4 - -928 NRAP NM_198060 10 - -406 NRG1 NM_013962 8 + -1308 NRK NM_198465 X + 910 NRN1 NM_016588 6 - 1231 NTRK2 NM_006180 9 + -1584 NTS NM_006183 12 + 696 NUDT11 NM_018159 X - 1498 NUP62CL NM_017681 X - 899 NXF3 NM_022052 X - -223 NXN NM_022463 17 - 1459 NXPH2 NM_007226 2 - 580 OCRL NM_001587 X + -531 ODAM NM_017855 4 + -1931 ODZ1 NM_014253 X - 454 OLFM3 NM_058170 1 - -65 OLIG1 NM_138983 21 + -1441 OPRD1 NM_000911 1 + -339 OPRM1 NM_000914 6 + -834 OR10AD1 NM_001004134 12 - 241 OR10C1 NM_013941 6 + -1170 OR10G2 NM_001005466 14 - -1163 OR10H2 NM_013939 19 + -1752 OR10H4 NM_001004465 19 + -1916 OR10P1 NM_206899 12 + -1941 OR10T2 NM_001004475 1 - -1621 OR11A1 NM_013937 6 - -1813 OR12D3 NM_030959 6 - 1246 OR1D2 NM_002548 17 - -1761 OR1J1 NM_001004451 9 - -1875 OR1J4 NM_001004452 9 + -339 OR1L3 NM_001005234 9 + 272 OR1N1 NM_012363 9 - -208 OR1N2 NM_001004457 9 + -768 OR1Q1 NM_012364 9 + 664 OR2B3 NM_001005226 6 - -597 OR2F1 NM_012369 7 + -451 OR2W1 NM_030903 6 - -950 OR2W5 NM_001004698 1 + -1551 OR2Y1 NM_001001657 5 - -537 OR4B1 NM_001005470 11 + 664 OR4D10 NM_001004705 11 + -1077 OR4D2 NM_001004707 17 + 1641 OR4K1 NM_001004063 14 + -1264 OR4K13 NM_001004714 14 - -1644 OR4K14 NM_001004712 14 - -1409 OR4K15 NM_001005486 14 + -616 OR4K2 NM_001005501 14 + -1565 OR4K5 NM_001005483 14 + 596 OR4L1 NM_001004717 14 + -1742 OR4N5 NM_001004724 14 + -1433 OR4Q3 NM_172194 14 + -825 OR51A4 NM_001005329 11 - -1095 OR51B6 NM_001004750 11 + -712

37 OR51E1 NM_152430 11 + -234 OR51E2 NM_030774 11 - 1056 OR51F1 NM_001004752 11 - -1578 OR51I1 NM_001005288 11 - -181 OR51M1 NM_001004756 11 + -203 OR51V1 NM_001004760 11 - 395 OR52A5 NM_001005160 11 - 53 OR52E2 NM_001005164 11 - -468 OR52I2 NM_001005170 11 + -1617 OR52N1 NM_001001913 11 - -1179 OR52N4 NM_001005175 11 + -1645 OR56A1 NM_001001917 11 - 709 OR5AU1 NM_001004731 14 - 277 OR5H14 NM_001005514 3 + -518 OR5U1 NM_030946 6 + -1944 OR5V1 NM_030876 6 - -1568 OR6C1 NM_001005182 12 + -949 OR6C2 NM_054105 12 + -563 OR6C3 NM_054104 12 + 550 OR6C6 NM_001005493 12 - -1618 OR6C65 NM_001005518 12 + -778 OR6C68 NM_001005519 12 + -512 OR6C70 NM_001005499 12 - -412 OR6C74 NM_001005490 12 + -537 OR6C75 NM_001005497 12 + 740 OR6C76 NM_001005183 12 + -403 OR6K2 NM_001005279 1 - 135 OR6K3 NM_001005327 1 - 624 OR6M1 NM_001005325 11 - -1334 OR6N2 NM_001005278 1 - -552 OR6S1 NM_001001968 14 - 411 OR8A1 NM_001005194 11 + -473 OR8D2 NM_001002918 11 - 398 OR8G1 NM_001002905 11 + -1331 OR9A2 NM_001001658 7 - 340 OR9K2 NM_001005243 12 + -18 OVCH1 NM_183378 12 - 1485 OVCH2 NM_198185 11 - 616 OXGR1 NM_080818 13 - -1796 P2RY12 NM_176876 3 - 26 PAGE4 NM_007003 X + -1342 PAK3 NM_002578 X + -554 PALM2 NM_053016 9 + -691 PALMD NM_017734 1 + 216 PAQR8 NM_133367 6 + 1298 PAX4 NM_006193 7 - -985 PBOV1 NM_021635 6 - 519 PCDH1 NM_002587 5 - 227 PCDH15 NM_033056 10 - -944 PCGF5 NM_032373 10 + 1153 PCK1 NM_002591 20 + -1441 PCOLCE2 NM_013363 3 - -277 PCSK9 NM_174936 1 + -406 PDCD8 NM_145813 X - -312

38 PDE1C NM_005020 7 - -585 PDE3A NM_000921 12 + -1162 PDE3B NM_000922 11 + 1595 PDE4B NM_002600 1 + 958 PDE4B NM_001037340 1 + 1224 PDHA2 NM_005390 4 + -1064 PECAM1 NM_000442 17 - 1922 PFDN4 NM_002623 20 + 1193 PHEX NM_000444 X + -540 PI15 NM_015886 8 + 1275 PI3 NM_002638 20 + -910 PKHD1 NM_138694 6 - 119 PKHD1L1 NM_177531 8 + -1280 PKIB NM_181795 6 + 826 PLA2G12B NM_032562 10 - 115 PLA2G2D NM_012400 1 - 494 PLA2G7 NM_005084 6 - -346 PLCB1 NM_182734 20 + -894 PLCXD3 NM_001005473 5 - -214 PLEK NM_002664 2 + 1774 PLEKHG1 NM_001029884 6 + -890 PLEKHK1 NM_145307 10 - 971 PLP1 NM_199478 X + 1992 Yes Membrane binding PLRG1 NM_002669 4 - 1172 PLUNC NM_130852 20 + -1961 PMP NM_153321 17 - 187 PMP22 NM_000304 17 - -432 PORCN NM_203476 X + -1213 POU2AF1 NM_006235 11 - -1074 POU4F2 NM_004575 4 + -1936 POU6F2 NM_007252 7 + -1831 PPARG NM_138711 3 + 1766 PPP1R3A NM_002711 7 - -601 PPP2CA NM_002715 5 - 1348 PRG4 NM_005807 1 + -199 PRIM1 NM_000946 12 - -1288 PRIMA1 NM_178013 14 - -1882 PRKAR2B NM_002736 7 + 1788 PRKCG NM_002739 19 + -1277 PRKG1 NM_006258 10 + -1597 PRKG2 NM_006259 4 - 562 PRODH2 NM_021232 19 - 1940 PROK1 NM_032414 1 + 91 PROK2 NM_021935 3 - 601 PROKR2 NM_144773 20 - 514 PROL1 NM_021225 4 + 1220 PROM1 NM_006017 4 - 1763 PROX1 NM_002763 1 + -1581 PRPS2 NM_002765 X + -1212 PSCDBP NM_004288 2 - -251 PSMAL NM_153696 11 + 389 PTGER3 NM_198715 1 - -1422 PTGIS NM_000961 20 - 1213 Yes Enzyme

39 PTH NM_000315 11 - -358 PTPRB NM_002837 12 - 90 PYHIN1 NM_198930 1 + -72 RAB33A NM_004794 X + 1848 RAB37 NM_175738 17 + -763 RAB8B NM_016530 15 + 1121 RAB9B NM_016370 X - 1513 RAG1 NM_000448 11 + 463 Yes Enzyme RAP2C NM_021183 X - -531 RARB NM_016152 3 + -556 RASEF NM_152573 9 - -638 RASGEF1A NM_145313 10 - -1828 RASGEF1C NM_001031799 5 - 1684 RASGRP1 NM_005739 15 - -1677 Yes Cell signaling RBBP5 NM_005057 1 - 1853 RBBP7 NM_002893 X - -1623 RBM17 NM_032905 10 + -911 RBM3 NM_006743 X + 1422 RDH10 NM_172037 8 + 1011 RDH12 NM_152443 14 + -1041 RFXDC1 NM_173560 6 + 633 RGN NM_152869 X + -1717 RGS7 NM_002924 1 - 1700 RGS9 NM_003835 17 + -582 RGSL1 NM_181572 1 + 461 RHAG NM_000324 6 - -1090 RIMS2 NM_014677 8 + -574 RIMS4 NM_182970 20 - -1575 RIT2 NM_002930 18 - 246 RNASE11 NM_145250 14 - 1556 RNASE3 NM_002935 14 + 0 RNF128 NM_024539 X + -522 RNF180 NM_178532 5 + 1775 RNF182 NM_152737 6 + 820 ROBO3 NM_022370 11 + 1510 ROPN1 NM_017578 3 - 488 ROPN1B NM_001012337 3 + 1084 RORB NM_006914 9 + -970 RP11- NM_001024609 13 + -1282 139H14.4 RP11- NM_017753 9 + 1064 35N6.1 RP11- NM_001010976 20 + -540 410N8.4 RP11- NM_173859 20 + -70 49G10.8 RP11- NM_015011 13 + 1 54H7.1 RP1L1 NM_178857 8 - -674 RPS6KA3 NM_004586 X - 1370 RSAD2 NM_080657 2 + -145 RUNX1T1 NM_175634 8 - 339 RXRG NM_001009598 1 - 1953 RYR3 NM_001036 15 + 1533

40 S100A9 NM_002965 1 + -1252 S100G NM_004057 X + -200 SAA4 NM_006512 11 - 491 SAGE1 NM_018666 X + -1149 SALL4 NM_020436 20 - 1420 SAMD12 NM_207506 8 - 1800 SAMD3 NM_001017373 6 - 591 SCGB1D1 NM_006552 11 + 216 SCGB2A2 NM_002411 11 + 396 SCGN NM_006998 6 + -1506 SCN10A NM_006514 3 - -1696 SCN2A2 NM_001040143 2 + 1973 SCN3A NM_006922 2 - -402 SCN7A NM_002976 2 - 577 SEC22B NM_004892 1 + 538 SEC63D1 NM_198550 1 - 1681 SEMA3E NM_012431 7 - 541 SEMA5B NM_001031702 3 - -1635 SEMG NM_198139 20 + -1886 SEMG1 NM_003007 20 + -86 SEMG2 NM_003008 20 + 1778 SERP1 NM_014445 3 - 1717 SERTAD4 NM_019605 1 + -716 SESN3 NM_144665 11 - 993 SFRS2IP NM_004719 12 - 586 SGCD NM_172244 5 + -143 SGPP1 NM_030791 14 - 1708 SH2D1A NM_002351 X + -373 SH3BGRL2 NM_031469 6 + 783 SH3GL2 NM_003026 9 + 908 SH3RF2 NM_152550 5 + 1467 SH3TC2 NM_024577 5 - 1529 SIGLEC6 NM_198846 19 - -125 SIRPG NM_001039508 20 - 1776 SKIP NM_030623 2 - 1885 SLAMF6 NM_052931 1 - 1465 SLC16A10 NM_018593 6 + -700 SLC16A9 NM_194298 10 - -935 SLC17A7 NM_020309 19 - 1495 SLC19A3 NM_025243 2 - -12 SLC1A1 NM_004170 9 + 1558 SLC1A2 NM_004171 11 - 1571 SLC1A7 NM_006671 1 - -1764 SLC22A10 NM_001039752 11 + -1193 SLC22A9 NM_080866 11 + 865 SLC26A5 NM_198999 7 - 1733 SLC27A6 NM_014031 5 + -1107 SLC34A1 NM_003052 5 + -259 SLC35F1 NM_001029858 6 + -1880 SLC37A3 NM_207113 7 - -1521 SLC43A2 NM_152346 17 - 1379 SLC44A3 NM_152369 1 + 1037 SLC4A10 NM_022058 2 + -490 SLC6A7 NM_014228 5 + -1211

41 SLC7A14 NM_020949 3 - -1549 SLC9A2 NM_003048 2 + -796 SLC9A4 NM_001011552 2 + -1692 SLC9A7 NM_032591 X - 1915 SLCO1C1 NM_017435 12 + -964 SLCO6A1 NM_173488 5 - -1182 SMAD5 NM_005903 5 + 1567 SMOC2 NM_022138 6 + -1078 SMR3B NM_006685 4 + -982 SNAP25 NM_130811 20 + 925 SNCB NM_003085 5 - -1838 SNTG1 NM_018967 8 + 852 SORL1 NM_003105 11 + 172 SOSTDC1 NM_015464 7 - 402 SOX21 NM_007084 13 - 1689 SOX5 NM_006940 12 - 203 SOX6 NM_033326 11 - 207 SPANX-N5 NM_001009616 X - 235 SPATA16 NM_031955 3 - 6 SPATA19 NM_174927 11 - -1599 SPATA9 NM_173360 5 - -1531 SPATS1 NM_145026 6 + 1038 SPINK1 NM_003122 5 - 52 SPINK2 NM_021114 4 - 449 SPO11 NM_198265 20 + 1564 SPRY1 NM_005841 4 + 969 SPZ1 NM_032567 5 + -1597 SRI NM_198901 7 - 643 ST3GAL6 NM_006100 3 + 1440 ST8SIA2 NM_006011 15 + -1042 ST8SIA4 NM_175052 5 - -632 STAC NM_003149 3 + 1601 STOX2 NM_020225 4 + 1999 STX11 NM_003764 6 + 1140 SUHW2 NM_080764 22 - -1796 SULF2 NM_198596 20 - -486 SULT2A1 NM_003167 19 - 296 SUNC1 NM_152782 7 - 1340 SUSD4 NM_001037175 1 - -1404 SYCP1 NM_003176 1 + -1976 SYNPR NM_144642 3 + -862 SYPL1 NM_182715 7 - 893 SYT10 NM_198992 12 - -1980 SYT3 NM_032298 19 - -1987 TAAR NM_014626 6 - 399 TAAR1 NM_138327 6 - -66 TAAR2 NM_001033080 6 - -194 TAAR6 NM_175067 6 + -152 TAAR8 NM_053278 6 + -223 TAAR9 NM_175057 6 + -818 TAF5L NM_001025247 1 - 1216 TAGAP NM_138810 6 - 971 TARP NM_001003806 7 - -1728 TBC1D21 NM_153356 15 + -419

42 TBX20 NM_020417 7 - 466 TCEAL2 NM_080390 X + 1886 TCEAL5 NM_001012979 X - -1245 TCEAL8 NM_153333 X - -424 TCF7 NM_213648 5 + 1476 TCL6 NM_020554 14 + 634 TCP10L NM_144659 21 - 314 TCTEX1D1 NM_152665 1 + -1928 TEKT1 NM_053285 17 - 783 TEX15 NM_031271 8 - 726 TFAP2B NM_003221 6 + -1640 TFEC NM_012252 7 - 933 TGM5 NM_201631 15 - 1546 TGM6 NM_198994 20 + -1952 THBS4 NM_003248 5 + 1555 TIMP1 NM_003254 X + 1968 TINAG NM_014464 6 + -360 TIP39 NM_178449 19 - -1291 TKTL2 NM_032136 4 - -1561 TMCC3 NM_020698 12 - -1246 TMEM10 NM_033207 10 - 1281 TMEM108 NM_023943 3 + 1059 TMEM16B NM_020373 12 - 58 TMEM16D NM_178826 12 + 986 TMEM56 NM_152487 1 + -270 TMEM74 NM_153015 8 - -55 TMOD2 NM_014548 15 + -1400 TNFRSF11B NM_002546 8 - 1091 TNFRSF19 NM_148957 13 + 879 TNFSF15 NM_005118 9 - -1772 TNPO1 NM_002270 5 + -1552 TP53BP2 NM_005426 1 - 1541 TPH1 NM_004179 11 - 1484 TPH2 NM_173353 12 + -391 TRAK1 NM_014965 3 + -1767 TRDN NM_006073 6 - -1160 TRIM55 NM_184087 8 + 1470 TRPM3 NM_001007471 9 - 1267 TSHB NM_000549 1 + 1864 TSLP NM_033035 5 + 413 TSPAN2 NM_005725 1 - 1437 TSPAN33 NM_178562 7 + -946 TSPAN6 NM_003270 X - -351 TTBK1 NM_032538 6 + -1598 TTC19 NM_017775 17 + 1595 TTC7B NM_001010854 14 - -587 TTLL2 NM_031949 6 + 1838 TTLL9 NM_001008409 20 + 1636 TTR NM_000371 18 + 464 TXNL5 NM_032731 17 + 951 TYR NM_000372 11 + 1514 UBE2A NM_181762 X + 1975 UBE2U NM_152489 1 + 1224 UBXD2 NM_014607 2 + 987

43 UGT2A1 NM_006798 4 - 305 UGT2B4 NM_021139 4 - 4 UGT8 NM_003360 4 + -1970 UMODL1 NM_173568 21 + 1165 UNC5C NM_003728 4 - 384 USH1C NM_153676 11 - -1362 USH3A NM_052995 3 - 288 USP11 NM_004651 X + 1544 USP15 NM_006313 12 + -1452 USP54 NM_152586 10 - 1103 VDR NM_001017535 12 - -720 VGLL2 NM_182645 6 + 772 VGLL4 NM_014667 3 - -464 VIP NM_003381 6 + -524 VSNL1 NM_003385 2 + 1014 VSTM2 NM_182546 7 + -140 VWA2 NM_198496 10 + -906 WDR67 NM_145647 8 + -1799 WFDC11 NM_147197 20 - 209 WFDC12 NM_080869 20 - 319 WFDC2 NM_080736 20 + 1794 WIF1 NM_007191 12 - 355 WNT2 NM_003391 7 - -1622 WNT4 NM_030761 1 - -904 WNT7A NM_004625 3 - -882 WNT8B NM_003393 10 + -1286 XAGE3 NM_130776 X - 1456 XAGE5 NM_130775 X + 1449 XKR7 NM_001011718 20 + -1464 YIPF7 NM_182592 4 - -886 YWHAB NM_139323 20 + 1744 ZCCHC23 NM_001039778 4 + 1062 ZFHX4 NM_024721 8 + -233 ZFP161 NM_003409 18 - 912 ZFX NM_003410 X + 1873 ZFYVE16 NM_014733 5 + 963 ZMAT1 NM_032441 X - 1448 ZMAT4 NM_024645 8 - 399 ZNF175 NM_007147 19 + -1241 ZNF22 NM_006963 10 + 1674 ZNF334 NM_199441 20 - -1400 ZNF416 NM_017879 19 - -746 ZNF502 NM_033210 3 + -640 ZNF521 NM_015461 18 - -1087 ZNF529 NM_020951 19 - -1271 ZNF645 NM_152577 X + 1121 ZNF648 NM_001009992 1 - -1031 ZNF654 NM_018293 3 + 1737 ZNF713 NM_182633 7 + -1123 ZNF75 NM_007131 X - 1022 Note: a) Only 19 of 1005 genes were found to associate with cancer using functional analysis performed by IPA software; b) A brief description of function for each gene related to cancer.

44 Table S5. Genes (n=723) downregulated by PI3K/AKT but without enrichment of H3K27me3 Expression Affymetrix folds Cancer b Gene Symbol a Function Prob_ID (AKT1 vs. Related Vector) ABAT 209459_s_at -2.65 Yes Enzyme ABCB7 209620_s_at -1.56 ABCD4 203981_s_at -1.68 ABHD12 228124_at -1.85 ABHD5 213805_at -1.77 ABI1 209027_s_at -1.63 ACAT2 209608_s_at -1.82 ACOT11 214763_at -1.57 ACP6 218795_at -1.62 ACSL3 201662_s_at -1.50 ACTG2 202274_at -3.23 ADA 204639_at -1.97 Yes Enzyme ADAMTS1 222162_s_at -4.65 Yes Peptidase AHNAK2 212992_at -1.52 AIM1 212543_at -4.09 Yes Relate to melanoma AKAP12 210517_s_at -3.12 Yes Transporter AKAP13 224884_at -2.42 Yes Kinase anchor protein AKAP9 210962_s_at -1.74 ALDH1A3 203180_at -3.95 Yes Enzyme ALDH6A1 221589_s_at -2.82 ALDH7A1 208950_s_at -1.67 ALPK1 227438_at -1.71 ALPK2 228367_at -3.43 ALPP 204664_at -9.07 Yes Phosphatase ALS2CL 229887_at -2.25 ALS2CR13 226431_at -2.00 ALS2CR4 228255_at -1.56 AMOTL2 203002_at -1.51 AMPD3 207992_s_at -3.24 ANXA8 203074_at -3.26 AOF2 238652_at -1.60 Yes Enzyme AP1G2 201613_s_at -1.96 APLP1 209462_at -1.51 APOL2 221653_x_at -1.79 APOLD1 221031_s_at -3.65 Yes Apolipoprotein ARHGAP23 226638_at -2.21 Rho guanine nucleotide ARHGEF3 218501_at -2.00 Yes exchange factor ARHGEF5 204765_at -1.88 ARHGEF9 203263_s_at -1.63 ARID5B 212614_at -1.88 ARL4A 205020_s_at -2.75 ARRDC4 225283_at -1.73 ATP1B1 201242_s_at -1.76 Yes Transporter ATP2B4 212136_at -4.03 ATXN3 235240_at -1.92 AURKA 204092_s_at -1.70 Yes Kinase

45 AVPI1 218631_at -1.78 AZI2 222498_at -1.56 B3GNT5 225612_s_at -2.03 B4GALT5 221485_at -2.22 Yes Enzyme BCL2-associated BAG1 229720_at -2.53 Yes athanogene BAIAP2L1 227372_s_at -3.31 BAZ2B 203080_s_at -2.48 BBS1 218471_s_at -1.51 BCL11A 222891_s_at -4.60 Yes Transcription regulator BCL2L11 1555372_at -2.54 Yes Apoptosis facilitator BCL2L2 209311_at -1.51 BCL6 203140_at -2.86 Yes Transcription regulator Baculoviral IAP repeat- BIRC5 202095_s_at -1.62 Yes containing 5 BRD8 202227_s_at -1.98 BTN2A2 205298_s_at -1.72 BTN3A2 204820_s_at -1.59 C10orf104 229145_at -1.78 C10orf118 227701_at -1.81 C10orf26 202808_at -1.80 C10orf30 227341_at -10.36 C10orf33 228384_s_at -2.25 Stress induced C10orf54 225373_at -3.52 Yes secreted protein C11orf67 221599_at -1.66 C11orf80 238593_at -2.39 C14orf147 213508_at -1.65 C14orf65 222809_x_at -2.01 C14orf94 218383_at -1.55 C18orf10 212055_at -1.66 C19orf21 212925_at -1.62 C19orf33 223631_s_at -1.63 C1orf106 219010_at -7.40 Protein-protein C1orf63 209006_s_at -1.53 Yes interactions C1orf85 1558692_at -1.66 C20orf199 226835_s_at -1.57 C21orf91 226109_at -2.48 C2orf33 223354_x_at -1.55 C2orf55 228067_at -1.78 C4orf14 223157_at -1.61 Golgi membrane FAM198B 223204_at -1.94 Yes protein C5orf13 201309_x_at -2.44 C6orf132 238028_at -1.92 C6orf48 220755_s_at -1.79 C7orf41 226018_at -1.63 C9orf140 225777_at -1.63 C9orf150 227443_at -1.96 CASP1 211368_s_at -2.23 Yes Peptidase CBFA2T2 238549_at -1.50 CBLB 209682_at -2.00 CBX4 227558_at -1.77

46 Chemokine C-C motif CCDC28A 209479_at -1.77 Yes receptor CCDC92 218175_at -1.53 CCNB1IP1 217988_at -1.54 CCNG2 211559_s_at -2.94 CCPG1 221511_x_at -2.50 CD2AP 203593_at -1.54 CD46 207549_x_at -1.70 Transmembrane CD9 201005_at -4.44 Yes protein CDC25B 201853_s_at -2.02 Yes Phosphatase CDC25C 205167_s_at -2.43 CDC42EP5 227850_x_at -14.32 CDCP1 218451_at -1.54 CDH1 201130_s_at -8.63 Yes Cell-cell adhesion CDH3 203256_at -20.66 Yes Cell-cell adhesion Cyclin-dependent CDKN1B 209112_at -2.08 Yes kinase inhibitor Cyclin-dependent CDKN1C 213348_at -33.46 Yes kinase inhibitor CDKN3 1555758_a_at -2.19 Yes Phosphatase CDS1 205709_s_at -11.64 CEBPD 203973_s_at -3.04 Yes Transcription regulator CELSR1 41660_at -2.30 CELSR2 204029_at -3.92 CENPF 207828_s_at -2.23 Yes Centromere protein CEP76 52285_f_at -1.62 CES2 209667_at -1.82 CG012 215318_at -1.84 CHD6 225031_at -1.77 CIT 212801_at -1.79 CKAP2 218252_at -1.72 CKB 200884_at -1.52 CKMT1A 202712_s_at -21.47 CLCC1 230002_at -2.62 CLDN1 222549_at -8.96 Yes Cell-to-cell adhesion CLDN7 202790_at -1.99 CLIC3 219529_at -27.23 CLK1 214683_s_at -1.72 Yes Kinase CMIP 224991_at -1.89 CNKSR1 204740_at -2.80 COG6 225769_at -1.64 COL17A1 204636_at -46.48 Yes Collagen COL1A1 202310_s_at -17.69 Yes Collagen COL4A1 211981_at -3.19 Yes Collagen COL4A2 211964_at -2.10 Yes Collagen COL4A3BP 223465_at -2.21 COL4A5 213110_s_at -2.16 COL7A1 204136_at -2.10 COL8A1 214587_at -1.54 CPA4 205832_at -2.19 Yes Peptidase CPM 235706_at -2.09 CPS1 217564_s_at -2.20 CREB3L4 226455_at -1.67

47 CREBL2 201989_s_at -1.60 Yes Transcription regulator CRISPLD2 221541_at -1.53 Cytoskeletal protein CRYAB 209283_at -2.35 Yes binding CSNK1A1 1556006_s_at -1.61 CSNK1D 208774_at -1.88 CSNK2A2 203575_at -1.92 Yes Kinase CSTA 204971_at -6.18 CTA-221G9.4 225525_at -3.36 CTDSP2 203445_s_at -2.29 CTDSPL 201906_s_at -1.54 Yes Phosphatase Cell adhesion and CTNND1 208407_s_at -1.57 Yes signal transduction CTPS2 219080_s_at -1.56 CTSK 202450_s_at -1.78 Yes Peptidase CUX1 214743_at -1.64 Yes Transcription regulator CYBRD1 217889_s_at -2.40 CYLD 221903_s_at -1.60 Yes Transcription regulator CYP1B1 202437_s_at -3.26 Yes Enzyme CYP1B1 202435_s_at -2.61 D4S234E 209570_s_at -2.40 DDAH2 214909_s_at -1.71 DDEFL1 222236_s_at -3.41 DDR1 1007_s_at -3.43 Yes Kinase DEPDC1 220295_x_at -2.25 Yes Signal transduction DEPDC1B 226980_at -1.81 DHCR24 200862_at -3.54 Yes Enzyme DHRS1 213279_at -1.79 DIAPH3 229097_at -1.57 Yes Enzyme DIRC2 226026_at -1.79 Yes Renal carcinoma DKFZp586I1420 213546_at -1.76 DKFZP761M1511 225355_at -9.91 DMKN 226926_at -8.48 DNAJB2 202500_at -1.91 Heat shock protein DNAJC15 218435_at -1.77 Yes binding DNAJC6 204720_s_at -7.92 DSG2 217901_at -1.94 Yes Cell-cell junctions DSP 200606_at -9.65 DST 204455_at -16.99 Yes Cell adhesion DTX4 212611_at -2.41 DUSP11 202703_at -1.64 DUSP14 203367_at -1.52 DUSP2 204794_at -2.47 Yes Phosphatase DYNC2LI1 203762_s_at -1.52 ECHDC2 218552_at -1.50 G-protein coupled EDG4 206723_s_at -2.72 Yes receptor EIF2C4 227930_at -2.21 EIF4EBP3 214919_s_at -1.55 ELAVL2 228260_at -2.39 ELMO3 219411_at -5.10 ELOVL5 208788_at -1.92 EPHA4 227449_at -4.33 Yes Kinase

48 ERBB2IP 222473_s_at -1.69 ERBB3 202454_s_at -13.71 Yes Kinase F11R 223000_s_at -10.67 FAM108B1 227551_at -1.56 FAM130A1 221260_s_at -1.58 FAM149B1 213463_s_at -1.73 Yes Related to lymphoma FAM33A 225684_at -1.75 FAM46B 229518_at -2.80 FAM59A 219377_at -2.18 FAM64A 221591_s_at -1.68 FAM83D 225687_at -1.81 FAM83H 226129_at -1.79 FBLIM1 225258_at -2.36 FBXL2 214436_at -1.55 Yes Enzyme FBXO2 219305_x_at -1.57 FBXO32 225803_at -15.17 FBXO8 223240_at -1.57 FBXW7 229419_at -2.05 Yes Transcription regulator FGD4 227948_at -2.47 Yes apoptosis FGD6 219901_at -2.41 FHDC1 226599_at -2.09 FHL1 201540_at -1.80 FLJ14213 219383_at -1.50 FLJ20160 225325_at -2.00 FLJ20209 226171_at -2.17 FLJ23867 226706_at -1.65 FLJ25778 225444_at -2.13 FLJ31818 228149_at -2.60 FLRT2 240259_at -4.87 Yes Cell adhesion Intracellular signaling FMN2 223618_at -3.48 Yes pathway FNBP1L 215017_s_at -2.31 FOLR3 206371_at -1.91 FOSL2 225262_at -2.60 Yes Transcription regulator FRAS1 226145_s_at -14.87 FRAT2 209864_at -1.69 FSTL1 208782_at -1.88 FXR1 201637_s_at -1.65 FZD2 210220_at -2.27 Insulin receptor GAB1 225998_at -2.46 Yes signaling pathway GABARAPL1 211458_s_at -8.30 GALNT2 239930_at -1.86 GALT 203179_at -1.56 GANC 236077_at -1.88 GAS1 204457_s_at -4.32 Yes Growth arrest GAS2L3 238756_at -2.54 GAS5 224841_x_at -1.55 GFOD1 219821_s_at -1.92 GJA1 201667_at -59.05 Yes Transporter GJB5 206156_at -7.63 GLCCI1 227525_at -2.51 GLS 203159_at -2.11 GLS 203158_s_at -1.74

49 GLTSCR2 217807_s_at -1.58 GOLGA2 225672_at -1.50 GOLGB1 201057_s_at -1.84 GPR56 212070_at -5.67 GPR64 206002_at -11.83 GPR87 219936_s_at -10.53 G-protein coupled GPRC5A 203108_at -1.64 Yes receptor G-protein signaling GPSM2 221922_at -2.80 Yes modulator GPX4 201106_at -1.76 Growth factor receptor- GRB10 209409_at -1.62 Yes bound protein GRK6 202848_s_at -2.09 GRLF1 229394_s_at -1.65 GSTA4 202967_at -2.67 Yes Enzyme GSTP1 200824_at -1.69 Yes Enzyme GTF2IRD1 218412_s_at -1.64 Imprinted tumor H19 224646_x_at -4.00 Yes suppressor H2AFV 202487_s_at -1.63 hCG_1776259 206548_at -2.10 HECA 218603_at -2.35 HEG1 212822_at -2.22 HES1 203394_s_at -3.81 Yes Transcription regulator HISPPD2A 1555255_a_at -1.68 HIVEP1 204512_at -1.76 Hyaluronan-mediated HMMR 209709_s_at -2.27 Yes motility receptor Heterogeneous nuclear HNRNPA1 214280_x_at -1.60 Yes ribonucleoprotein HOOK2 218780_at -1.62 HOXA3 235521_at -1.61 Yes Transcription regulator HOXC13 219832_s_at -1.97 HOXC4 206194_at -2.01 Yes Transcription regulator HOXC6 206858_s_at -1.67 Yes Transcription regulator HP1BP3 224591_at -1.62 HS6ST1 225263_at -1.88 HSD17B11 217989_at -1.91 Yes Enzyme HSD17B12 217869_at -1.52 HSD17B8 213540_at -1.53 HSPB1 201841_s_at -2.59 Yes Heat shock protein HSPG2 201655_s_at -1.88 HTATIP2 207180_s_at -1.57 Yes Transcription regulator ID3 207826_s_at -1.91 Interferon, alpha- IFI27 202411_at -6.61 Yes inducible protein IFI30 201422_at -2.03 Yes Enzyme IGFL2 231148_at -1.86 IHPK2 218192_at -1.92 IKZF2 231929_at -1.83 Yes Transcription regulator INADL 223681_s_at -4.92 INPP5D 203332_s_at -6.13 Yes Phosphatase

50 INSIG1 201625_s_at -1.53 Yes Insulin induced gene IQGAP3 229538_s_at -2.57 IQWD1 217908_s_at -1.67 IRF9 203882_at -1.65 IRX2 228462_at -2.91 IRX4 220225_at -4.49 IRX5 210239_at -1.71 ITCH 239101_at -1.75 ITGA6 215177_s_at -2.30 Yes Cell adhesion ITGAV 202351_at -1.57 Yes Cell adhesion ITGB4 204990_s_at -4.76 Yes Cell adhesion ITSN1 209298_s_at -1.51 JAG2 209784_s_at -1.77 Yes Growth factor JHDM1D 221778_at -1.84 JMJD1C 228793_at -2.47 JUND 203752_s_at -2.07 Yes Transcription regulator JUP 201015_s_at -10.81 Yes Junction plakoglobin KCNK6 223658_at -1.81 Yes Ion channel KIAA0182 212056_at -1.86 KIAA0265 209255_at -1.56 KIAA0427 204303_s_at -1.78 KIAA0513 204546_at -1.61 KIAA0828 212814_at -1.63 KIAA0831 204568_at -1.73 KIAA1109 212779_at -1.81 KIAA1522 224746_at -3.61 Tet oncogene family KIAA1546 227624_at -1.98 Yes member KIAA1659 215750_at -3.38 KIAA1712 228334_x_at -1.59 KIDINS220 212163_at -1.56 Yes Transcription regulator KIF11 204444_at -1.55 Yes kinesin KIF18A 221258_s_at -1.75 KIF2C 209408_at -1.57 KIF3C 203390_s_at -2.53 KIF3C 203389_at -1.73 KIF4A 218355_at -1.78 KITLG 226534_at -2.11 Yes Growth factor KLC3 239853_at -3.12 KLF13 225390_s_at -1.63 KLF3 225133_at -1.75 KLHDC2 217906_at -1.60 KLHL24 226158_at -7.26 KRCC1 218303_x_at -1.51 KRT15 204734_at -10.13 KRT17 205157_s_at -69.83 Yes Protein binding Structural constituent of KRT6B 213680_at -26.85 Yes cytoskeleton KRTCAP3 235148_at -2.69 LAMB2 216264_s_at -2.36 LAMB3 209270_at -1.88 LAMC2 207517_at -5.31 Yes Cell adhesion LASS6 212446_s_at -2.41

51 Cervical cancer LETMD1 207170_s_at -1.96 Yes protooncogene LFNG 228762_at -3.06 LGMN 201212_at -1.99 LIN7B 241957_x_at -2.70 LITAF 200704_at -2.24 LNX2 227569_at -1.70 LOC126917 225615_at -2.12 LOC145842 226358_at -1.53 LOC253039 231828_at -2.00 LOC254128 235132_at -1.84 LOC283357 235151_at -2.16 LOC284356 1555842_at -1.97 LOC285812 230179_at -2.08 LOC286161 228615_at -1.73 LOC375190 230435_at -1.66 LOC388969 221878_at -1.81 LOC401805 238949_at -2.31 LOC440087 237484_at -9.20 LOC440498 232594_at -1.56 LOC440934 238727_at -1.67 LOC440995 235911_at -2.50 LOC553103 241899_at -1.53 LOC56755 232135_at -1.57 LOC56757 225509_at -1.93 LOC642587 226755_at -37.45 LOC645638 229566_at -3.20 LOC653110 1557094_at -4.58 LOC728193 219987_at -1.83 LOC728377 228596_at -2.01 LOC728903 228040_at -1.57 LOC729013 235010_at -1.65 LOC729446 238043_at -1.63 LOC729570 227837_at -1.53 LOC730391 230653_at -1.58 LOC90110 226842_at -1.57 LOC92482 228993_s_at -2.24 Breast cancer LOH11CR2A 210102_at -2.64 Yes suppressor LPCAT1 201818_at -1.91 LPIN1 212274_at -2.71 Transmembrane LRP1 200785_s_at -1.67 Yes receptor LRP11 225060_at -1.63 LRRC1 218816_at -2.37 LRRFIP1 223492_s_at -1.75 LUZP1 221832_s_at -1.94 LXN 218729_at -2.22 LYPD3 204952_at -6.07 LYST 203518_at -2.71 MALAT1 224558_s_at -2.32 Yes Associated metastasis MALT1 210017_at -1.56 MAP2 225540_at -10.81 Yes Structural molecule MAP3K1 225927_at -1.72 Yes Kinase

52 TGF-beta activated MAP3K7IP3 227357_at -1.61 Yes kinase binding protein MAP4K3 218311_at -1.57 MAP4K5 203552_at -1.56 MARCKSL1 200644_at -3.68 MARVELD2 235141_at -2.20 MAST4 225613_at -2.97 MBTD1 226797_at -2.20 MCC 226225_at -3.85 MED13L 212209_at -1.71 MEGF6 226869_at -5.35 MEGF9 212830_at -1.64 Yes EGF-like-domains MEIS1 204069_at -3.04 Yes Transcription regulator METTL7A 207761_s_at -4.06 MFI2 223723_at -1.68 MFN1 217043_s_at -1.52 Yes Enzyme MGC16121 228235_at -2.88 MGC20769 210139_s_at -4.19 MGC33894 226657_at -2.48 MGC5618 221477_s_at -2.04 MICALL1 55081_at -1.67 Yes Metal ion binding MKL2 218259_at -1.98 MKRN1 209845_at -1.60 MLL5 226100_at -1.57 Myeloid/lymphoid or MLLT3 204917_s_at -2.21 Yes mixed-lineage leukemia MMP28 239272_at -3.48 MPDZ 205079_s_at -1.57 MPPE1 213924_at -2.12 Transmembrane MR1 210224_at -1.64 Yes receptor MRC2 37408_at -1.51 MSLN 204885_s_at -2.40 Yes Extracellular protein MTMR10 225810_at -2.14 MTMR3 202197_at -1.60 MTSS1 203037_s_at -2.73 MYL7 219942_at -2.51 MYO5B 225301_s_at -6.63 MYO6 203216_s_at -1.72 NANOS1 228523_at -1.97 NAV2 218330_s_at -1.82 NBR1 201384_s_at -1.54 NDE1 227249_at -1.90 Yes Protein binding NEK2 204641_at -2.52 Yes Kinase NFE2L1 214179_s_at -1.98 Yes Transcription regulator NIPBL 212483_at -1.52 NOTCH1 218902_at -1.59 Yes Transcription regulator NPAL3 225875_s_at -1.57 NUAK1 204589_at -1.92 Yes Kinase NUCB2 229838_at -1.53 NUDT1 204766_s_at -1.60 Yes Phosphatase NUDT13 214136_at -2.45 NUDT14 231914_at -1.81

53 Nucleolar and spindle NUSAP1 218039_at -1.85 Yes associated protein OBSL1 212775_at -1.51 OCIAD2 225314_at -1.67 OFD1 203569_s_at -1.65 OPN3 219032_x_at -1.77 OPTN 202073_at -2.31 OSBPL2 209221_s_at -1.93 OTUD1 226140_s_at -4.72 P2RY5 218589_at -2.97 PAK6 1555310_a_at -3.65 PAN2 203117_s_at -1.64 PAPOLG 222273_at -1.60 PAPSS2 203060_s_at -12.70 Yes Enzyme PATZ1 209431_s_at -1.56 PBXIP1 214177_s_at -2.68 PCDH7 228640_at -2.97 PCDHA1 210674_s_at -1.71 PCGF3 212753_at -1.60 PCMTD1 226119_at -2.27 PCMTD2 212406_s_at -1.93 PCSK6 207414_s_at -2.43 Yes Peptidase PDCD4 202731_at -2.91 Yes Programmed cell death PDE4DIP 214130_s_at -1.63 PDK2 202590_s_at -2.23 PDLIM1 208690_s_at -2.38 Ubiquitin-protein ligase PELI1 218319_at -1.62 Yes activity PERP 217744_s_at -3.03 Yes Apoptosis PGD 201118_at -1.57 PGRMC2 213227_at -1.51 PHF17 225816_at -2.01 PIF1 228252_at -2.91 PIGV 51146_at -1.73 PIK3CA 204369_at -1.55 Yes Kinase PIK3CD 203879_at -2.13 Yes Kinase PILRB 225321_s_at -2.06 PIM1 209193_at -1.98 Yes Kinase PKIG 202732_at -2.01 PKP2 207717_s_at -10.69 PKP3 209873_s_at -2.92 PLD1 226636_at -3.05 PLSCR1 202446_s_at -1.82 PLSCR4 218901_at -3.52 Yes Enzyme PLXNA1 221538_s_at -1.50 PNPLA8 223982_s_at -1.52 Nuclear receptor PNRC1 209034_at -2.02 Yes coactivator POLR1D 224874_at -1.77 PPM1B 213225_at -2.71 PPP1R13L 218849_s_at -1.63 Yes Transcription regulator PPP4R2 226317_at -1.61 PRC1 218009_s_at -1.70 Yes Cell cycle PRCP 201494_at -1.52

54 PRKCZ 202178_at -3.93 Yes Kinase PRO1073 223577_x_at -1.55 PROM2 1552797_s_at -6.03 PRR11 219392_x_at -1.54 PRRG1 205618_at -2.22 PRRG4 238513_at -3.05 PRSS23 229441_at -2.05 Yes Peptidase PRSS8 202525_at -8.99 PRUNE 210988_s_at -1.67 PRUNE2 212805_at -3.06 Yes Oxidoreductase activity PSCD2 209158_s_at -1.63 PSCD3 225147_at -2.05 PSG1 208257_x_at -1.62 PSG3 215821_x_at -1.82 PSG4 208191_x_at -2.37 PSG5 204830_x_at -2.83 PSMB8 209040_s_at -2.17 PSTPIP2 219938_s_at -1.84 PTEN 211711_s_at -1.62 Yes Phosphatase PTGES 210367_s_at -2.37 Yes Enzyme PTK2B 203110_at -1.54 PTK7 207011_s_at -1.74 PTPN13 204201_s_at -1.81 PTPN6 206687_s_at -1.82 Yes Phosphatase PTPRS 226571_s_at -1.59 PTTG1 203554_x_at -2.41 Yes Transcription regulator PVT1 1558290_a_at -1.62 Yes Oncogene PYGL 202990_at -1.85 RAB11A 200864_s_at -1.59 RAB7B 230266_at -8.20 Small GTPase RALGDS 209050_s_at -1.77 Yes regulator activity RAPGEFL1 218657_at -2.23 RASSF5 223322_at -2.31 Yes Apoptosis RBM35B 219395_at -6.82 REEP4 218777_at -1.87 REL 206036_s_at -3.37 Yes Transcription regulator RERE 200940_s_at -1.60 RFX2 226872_at -2.20 RFX5 202963_at -2.03 RGNEF 232994_s_at -1.67 RGS2 202388_at -3.95 Yes GTPase activator RHOD 209885_at -3.29 RIOK3 202130_at -1.57 RIPK5 229017_s_at -1.99 RIPPLY2 223740_at -1.57 RNASE4 205158_at -2.06 RNF144B 228153_at -6.14 Yes Enzyme RNF44 203286_at -1.68 Yes Metal ion binding RNF5 209111_at -1.72 ROS1 207569_at -1.61 Yes Kinase

RP11-298P3.3 214748_at -1.90

55 RP11-345P4.4 217122_s_at -1.75 RPAIN 228183_s_at -1.55 RPS6KA1 203379_at -1.82 Yes Kinase RRAGC 218088_s_at -1.56 RRAS2 212589_at -1.84 Yes Enzyme RTKN 225150_s_at -2.39 RUFY3 213939_s_at -2.10 Chemokine receptor S100A14 218677_at -41.88 Yes binding calcium-dependent S100P 204351_at -3.96 Yes protein binding SAA 208607_s_at -1.96 SAA1 214456_x_at -2.69 Yes Transporter SAMD4A 212845_at -1.62 SAMD9 228531_at -1.95 SAT2 225272_at -1.53 Yes Enzyme SATB1 203408_s_at -2.08 SC4MOL 209146_at -2.40 Yes Enzyme SCLT1 236487_at -1.64 SCNN1A 203453_at -4.11 SCNN1G 241436_at -1.81 SCPEP1 218217_at -1.50 Cytoskeletal protein SDC1 201286_at -2.35 Yes binding SDPR 222717_at -2.40 Yes Phospholipid binding SEPT6 212414_s_at -2.89 SERTAD2 202657_s_at -1.62 Yes Transcription regulator SESN1 218346_s_at -2.00 SETDB1 203155_at -1.51 Protein kinase C SFN 209260_at -3.89 Yes inhibitor SGCE 204688_at -1.92 SH3BGRL 201311_s_at -2.32 SH3BP5 201811_x_at -3.48 SHOX2 210135_s_at -2.79 SIDT2 56256_at -1.95 Yes Membrane protein SIN3B 39705_at -1.51 SIX2 206510_at -3.42 SLC12A8 219874_at -2.44 Yes Transporter SLC16A14 238029_s_at -1.62 SLC24A1 206081_at -2.36 SLC27A1 226728_at -1.61 SLC2A5 204430_s_at -10.50 Yes Transporter SLC39A10 225295_at -1.95 SLC44A2 224609_at -2.73 SLC44A5 235763_at -4.30 SLC7A11 217678_at -3.23 Yes Transporter SLCO1B3 206354_at -14.10 Yes Transporter SLITRK6 232176_at -3.42 SMAD3 218284_at -2.78 Yes Transcription regulator SMAD6 207069_s_at -2.53 SMARCD2 201827_at -1.52 SMPDL3A 213624_at -2.21

56 SNF1LK 208078_s_at -1.70 Yes Kinase SNHG7 229050_s_at -1.66 SNHG8 225220_at -2.00 SNN 218032_at -3.96 SNX21 1553960_at -1.84 SOD2 1566342_at -1.89 Yes Enzyme SOX4 201417_at -1.90 Yes Transcription regulator SPAG5 203145_at -1.62 SPARC 200665_s_at -22.55 Yes Extracellular protein SPATA7 219583_s_at -1.77 SPIN1 222431_at -1.53 SPRR1A 214549_x_at -8.27 Intracellular signaling SPSB1 226075_at -7.58 Yes pathway SPSB3 46256_at -1.70 SPTLC2 225095_at -1.88 SQLE 213562_s_at -2.32 Yes Enzyme SRGAP2 213329_at -1.77 SRGAP2P1 232095_at -1.71 SRPK2 203182_s_at -1.74 SSBP2 203787_at -1.68 SSH3 219919_s_at -1.71 ST5 202440_s_at -1.85 Yes Enzyme ST7 207871_s_at -1.77 STAG2 209022_at -1.52 STAG3L1 221191_at -1.58 STAG3L4 222801_s_at -1.50 STAP2 221610_s_at -2.05 STARD10 223103_at -3.28 STARD4 226390_at -2.27 STAT2 225636_at -1.99 Yes Transcription regulator STOM 201061_s_at -2.48 Yes protein binding STON2 227461_at -1.76 STX17 228091_at -1.62 SUDS3 224974_at -1.51 SUV420H1 222566_at -1.75 Yes Enzyme SWAP70 209307_at -2.09 SYTL1 227134_at -5.97 Nuclear hormone TACC2 211382_s_at -1.87 Yes receptor binding Tumor-associated TACSTD2 202286_s_at -12.25 Yes calcium signal transducer TAF9B 226037_s_at -2.18 TAGLN 205547_s_at -2.03 Yes Actin binding TAP1 202307_s_at -1.66 TAP2 225973_at -1.88 TAPBP 208829_at -1.68 TBC1D3 209403_at -1.53 TCF7L2 216511_s_at -2.44 Yes Transcription regulator TESK2 205486_at -1.99 TEX2 218099_at -1.64 TFDP2 226157_at -2.44 Yes Transcription regulator TGFBR3 204731_at -2.31 Yes Kinase

57 TGM2 201042_at -3.23 THSD1 219477_s_at -2.28 TIMP metallopeptidase TIMP3 201150_s_at -5.39 Yes inhibitor TJP1 202011_at -1.53 TMEM157 226752_at -1.68 TMEM30B 213285_at -9.50 TMPRSS11E 220431_at -7.23 TMTC3 226604_at -1.73 TNC 201645_at -1.90 Yes Cell adhesion TncRNA 224566_at -1.70 TNFAIP8L1 227420_at -3.39 TNNT1 213201_s_at -2.67 TNS4 230398_at -1.76 Yes Apoptosis TOB1 202704_at -1.56 Yes Transcription regulator TOP2A 201292_at -2.00 Yes Enzyme TP53AP1 209917_s_at -2.49 TP63 209863_s_at -25.32 Yes Transcription regulator TRAF3IP2 215411_s_at -2.05 TRAPPC6A 204985_s_at -1.88 TRIM5 210705_s_at -1.73 TRIM59 227801_at -1.88 TRIM73 1554250_s_at -1.83 TROAP 204649_at -2.43 TTBK2 1557073_s_at -1.66 TUBD1 231853_at -1.81 Yes GTPase activity TUFT1 205807_s_at -2.47 TWSG1 219201_s_at -1.59 UBE2C 202954_at -1.85 Yes Enzyme UBE2H 222421_at -2.39 UBR2 212760_at -1.65 UBR5 208884_s_at -1.57 Yes Enzyme UBTD2 224827_at -1.53 UBXD1 223012_at -1.52 UGCG 224967_at -2.03 Yes Enzyme UGT1A1 215125_s_at -9.15 Yes Enzyme ULK1 209333_at -1.71 ULK2 204062_s_at -2.68 UNC84B 212144_at -1.75 USP47 223117_s_at -1.58 USP9X 201099_at -1.52 Yes Peptidase UTX 203992_s_at -1.67 VAV3 218807_at -19.95 Yes Cytokine VCAN 221731_x_at -8.37 Yes Cell adhesion VGLL3 220327_at -1.74 VPS13A 227988_s_at -1.52 VPS13D 212324_s_at -1.53 WBP2 209117_at -2.01 WDR19 220917_s_at -1.83 Yes Signal transduction WDR59 218505_at -1.55 WEE1 215711_s_at -1.52 Yes Kinase WISP1 206796_at -5.96 Yes Signal transduction XRN1 225814_at -1.98 YPEL3 223179_at -5.01

58 YPEL5 222408_s_at -2.23 Yes Cell division ZBED2 219836_at -21.30 ZBTB10 228562_at -1.64 ZBTB22 213081_at -1.50 Regulation of ZBTB4 225629_s_at -1.61 Yes transcription ZBTB5 203026_at -1.74 ZC3H6 227809_at -2.22 ZDHHC17 212982_at -1.73 Yes Enzyme ZDHHC3 236507_at -2.07 ZFAND5 210275_s_at -2.37 ZFHX3 226137_at -1.74 Yes Transcription regulator ZFP90 235698_at -1.73 ZNF266 214686_at -1.53 ZNF277 218645_at -2.39 ZNF304 207753_at -1.51 ZNF362 226820_at -1.82 ZNF385B 1555800_at -14.11 ZNF436 226113_at -2.75 ZNF462 226575_at -1.60 ZNF550 228099_at -1.55 ZNF57 1554628_at -1.56 ZNF581 223389_s_at -1.95 ZNF655 225945_at -1.69 ZNF85 206572_x_at -1.72 Note: a) Analysis performed by IPA software identified 207 of 723 genes related to cancer; b) A brief description of function of each cancer associated gene was listed.

59 Table S6. Summary of 21 breast cancer cell lines

Cell Cell lines HER2 ER PR Pathology Age Gender Ethnicity type

BT-474 Lu Pos. Pos. Pos. Invasive ductal carcinoma 60 Female Caucasian

UACC-812 Lu Pos. Pos. Neg. Ductal carcinoma 43 Female N/A

Breast adenocarcinoma; MCF7 Lu Neg. Pos. Pos. derived from metastatic pleural 69 Unknow Caucasian effusion. Breast adenocarcinoma; MDA-MB-361 Lu Pos. Pos. Neg. derived from metastatic site at 40 Female Caucasian brain Infiltrating ductal carcinoma; T-47D Lu Neg. Pos. Pos. derived from metastatic pleural 54 Female N/A effusion

BT-20 BaA Neg. Neg Neg. Breast carcinoma 74 Female Caucasian

Breast adenocarcinoma; MDA-MB-453 Lu Pos. Neg Neg. derived from metastatic 48 Female Caucasian pericardial effusion SUM159PT BaB Neg. Neg Neg. Anaplastic carcinoma N/A N/A N/A

HCC1954 BaA Pos. Neg Neg. Ductal carcinoma 61 Female Indian

HCC70 BaA Neg. Neg. Neg. Invasive ductal carcinoma 49 Female Black

Ductal carcinoma; derived from ZR-75-1 Lu Neg. Pos. Neg. 63 Female Caucasian metastatic ascites effusion

BT-549 BaB Neg. Neg Neg. Invasive ductal carcinoma 72 Female Caucasian

Breast adenocarcinoma; MDA-MB-468 BaA Neg. Neg Neg. derived from metastatic pleural 51 Female Black effusion.

HCC1937 BaA Neg. Neg Neg. Ductal carcinoma 23 Female Caucasian

Breast adenocarcinoma; MDA-MB- Lu Neg. Pos. Neg. derived from metastatic pleural 47 Female Caucasian 134-VI effusion. Breast adenocarcinoma; SK-BR-3 Lu Pos. Neg Neg. derived from metastatic pleural 43 Female Caucasian effusion. HCC1500 BaB Neg. Neg. Neg. Ductal carcinoma 32 Female Black

HCC1187 BaA Neg. Neg. Neg. Invasive ductal carcinoma 41 Female Caucasian Breast adenocarcinoma; MDA-MB-231 BaB Neg. Neg. Neg. derived from metastatic pleural 51 Female Caucasian effusion. Hs578T BaB Neg. Neg. Neg. Breast carcinoma 74 Female Caucasian

SUM149PT BaB Neg. Neg. Neg. Invasive ductal carcinoma N/A N/A N/A

Abbreviations: BaA: Basal A ; BaB: Basal B; ER: Estrogen receptor; fs: frame shift; Lu: luminal; N/A: not available; Neg.: Negative; Pos.: Positive; PR: Progesterone receptor.

60 Note: A total of 21 breast cancer cell lines were cultured by following instructions described previously (Neve et al., 2006; Cited in main text). The general information of cell lines was obtained from AATC (http://www.atcc.org).

61 Table S7. Summary of in silico expression values of 180 genes in 21 breast cancer lines and 4 normal human mammary epithelial cell samples (HMECs) b c Down- a Cancer lines HMECs e Gene Symbol regulation p value d Mean STDEV Mean STDEV folds ► MAOA 23 9 898 327 38.7 3.E-17 ► MAF 8 2 114 57 14.6 1.E-14 GPR1 9 1 33 9 3.7 1.E-14 FLRT3 13 4 809 540 64.4 4.E-14 ► PROS1 13 9 166 67 12.6 2.E-11 SPRR1B 65 142 5437 2152 84.2 2.E-10 ► CROT 29 5 118 59 4.0 4.E-10 C1RL 14 6 81 17 5.8 5.E-10 C20orf19 65 16 440 251 6.8 5.E-10 ► HOXA9 15 17 234 80 15.4 5.E-10 MFAP5 12 1 45 23 3.9 6.E-10 KRT6A 72 127 2629 1135 36.5 8.E-10 COL4A6 27 13 252 132 9.5 1.E-09 LTA4H 483 147 2538 505 5.3 1.E-09 ► CA2 60 68 3558 1458 59.0 2.E-09 ► LARP6 54 17 266 91 4.9 2.E-09 IL1RN 78 53 2253 1769 28.8 3.E-09 ERMAP 17 3 46 10 2.8 5.E-09 ► GNAI1 17 10 174 51 10.2 5.E-09 ► DFNA5 52 48 817 237 15.8 5.E-09 EVA1 21 18 668 419 31.2 7.E-09 DSG3 34 40 1124 736 32.8 7.E-09 C1orf116 40 20 361 179 9.0 8.E-09 CALD1 17 13 244 69 14.6 9.E-09 MARK4 110 35 386 47 3.5 2.E-08 IGBP1 182 77 851 210 4.7 2.E-08 ► DSC2 28 23 1024 688 36.5 3.E-08 CEP68 27 9 84 5 3.1 3.E-08 BDH2 67 28 325 62 4.8 6.E-08 SERPINB-13 35 23 538 409 15.4 6.E-08 PALLD 48 22 278 109 5.8 9.E-08 FGFBP1 172 206 3600 2047 20.9 1.E-07 RAB9A 182 81 943 309 5.2 1.E-07 FYN 65 55 587 170 9.0 2.E-07 ► PIR 59 43 507 151 8.6 3.E-07 SCEL 13 15 242 180 18.1 3.E-07 GM2A 209 93 911 331 4.4 4.E-07 BTG1 273 184 1854 344 6.8 4.E-07 ZNF419 45 15 143 49 3.2 4.E-07 ► TNFAIP8 30 14 171 59 5.7 4.E-07 ► PLEKHA1 58 27 318 139 5.5 4.E-07 ► KLF5 25 32 434 255 17.4 6.E-07 KRT16 176 460 4496 2287 25.6 1.E-06 CENTD1 15 5 112 65 7.4 1.E-06 ► IL6R 15 3 29 4 2.0 1.E-06 MKL1 63 13 120 18 1.9 1.E-06 IRF6 251 117 2005 1506 8.0 2.E-06 ► AUH 63 29 207 29 3.3 2.E-06 ZNF185 160 73 1219 695 7.6 2.E-06

62 ► ETS2 46 27 296 126 6.5 2.E-06 CTSL2 132 79 1627 1750 12.3 2.E-06 KIAA0746 63 46 361 63 5.7 2.E-06 ITGB6 27 25 230 190 8.6 2.E-06 ► ANKRA2 40 20 128 16 3.2 3.E-06 TRIM29 250 386 2658 1213 10.6 4.E-06 KRT14 453 1169 9814 2394 21.7 5.E-06 COL3A1 152 479 1909 2074 12.6 6.E-06 AGA 18 10 70 22 3.8 7.E-06 RGC32 15 8 104 108 7.0 7.E-06 CD55 137 102 1127 514 8.2 7.E-06 CUL4B 51 32 224 147 4.4 8.E-06 KIAA0430 50 28 159 23 3.1 9.E-06 CLCA2 93 264 914 490 9.8 9.E-06 GRAMD3 49 27 335 211 6.8 1.E-05 ► LAMB1 59 58 576 353 9.7 1.E-05 PHF20 78 25 178 20 2.3 1.E-05 KIAA1128 43 16 136 49 3.2 1.E-05 TES 106 57 516 176 4.9 1.E-05 ALDH3A2 158 88 515 175 3.3 1.E-05 ► HOXA5 49 20 152 62 3.1 1.E-05 ANXA3 101 117 1540 907 15.2 2.E-05 TNFRSF21 43 32 207 31 4.8 2.E-05 ► SMARCA1 22 25 113 57 5.0 2.E-05 ► PLEKHA5 45 29 244 98 5.4 2.E-05 ► RGS12 64 15 138 66 2.2 2.E-05 ► LPHN2 34 29 209 103 6.2 3.E-05 GADD45A 249 240 1681 757 6.7 3.E-05 S100A2 580 1078 9618 2308 16.6 3.E-05 EPS8L2 172 89 708 166 4.1 4.E-05 GJB3 94 88 645 506 6.8 4.E-05 IMPA2 183 149 959 249 5.2 4.E-05 CREG1 349 218 2036 667 5.8 4.E-05 SLPI 829 1583 8353 3033 10.1 5.E-05 RECK 9 3 30 29 3.4 5.E-05 STX7 72 34 215 68 3.0 5.E-05 COBLL1 31 18 169 105 5.5 5.E-05 PPL 177 137 1330 603 7.5 6.E-05 ABCA12 30 55 342 287 11.4 6.E-05 LRRFIP2 99 29 223 85 2.3 7.E-05 LEPREL1 156 172 1246 632 8.0 7.E-05 ► NEDD4L 48 15 93 24 1.9 7.E-05 ► LIMK2 78 57 332 120 4.2 8.E-05 ► BTG2 120 70 338 108 2.8 9.E-05 ► SFRP1 65 87 267 63 4.1 9.E-05 MBNL2 49 28 127 27 2.6 9.E-05 TLE1 42 19 91 14 2.2 1.E-04 ► PAWR 45 26 156 71 3.5 1.E-04 KRT5 695 1258 8172 2300 11.8 1.E-04 CARD10 95 65 293 42 3.1 1.E-04 RGS10 122 75 429 193 3.5 1.E-04 DNAJB9 105 59 308 24 2.9 1.E-04 FDFT1 545 298 1568 292 2.9 2.E-04 SOS2 66 26 167 65 2.5 3.E-04 JAG1 138 173 858 415 6.2 3.E-04 ABLIM1 189 152 1578 1235 8.3 3.E-04 CLCN3 156 89 398 144 2.6 4.E-04

63 LANCL1 191 140 492 151 2.6 4.E-04 TRIM22 38 78 207 163 5.4 4.E-04 ► CSRP2 91 138 409 192 4.5 5.E-04 FXYD3 277 96 619 245 2.2 5.E-04 DLG5 209 84 491 142 2.4 6.E-04 DAB2 52 34 163 111 3.1 6.E-04 TOM1L1 141 157 578 263 4.1 6.E-04 ► LOX 92 226 313 171 3.4 6.E-04 AKR1C3 218 524 934 278 4.3 6.E-04 IGFBP2 273 305 1679 799 6.2 7.E-04 S100A8 1098 1735 8792 3313 8.0 1.E-03 CLDND1 92 56 251 90 2.7 1.E-03 ► F2RL1 95 130 420 196 4.4 1.E-03 TSC22D3 337 287 1358 1022 4.0 1.E-03 ► CST6 87 180 371 283 4.2 1.E-03 CXorf12 75 32 167 51 2.2 1.E-03 TPM1 225 177 570 260 2.5 1.E-03 CSGALNACT1 33 29 143 130 4.4 1.E-03 COL5A2 86 241 276 243 3.2 2.E-03 RABGAP1 178 82 473 223 2.7 2.E-03 ► TLE4 47 49 128 36 2.7 2.E-03 FAM8A1 99 43 182 44 1.8 3.E-03 LMBRD1 245 115 486 154 2.0 3.E-03 GPR137B 48 36 114 31 2.4 3.E-03 ► CTGF 155 279 495 276 3.2 3.E-03 LIMA1 280 102 617 267 2.2 3.E-03 IL15 19 8 59 47 3.0 3.E-03 CLK4 50 29 95 36 1.9 3.E-03 ZNF532 104 64 204 59 2.0 5.E-03 SNX13 82 26 133 36 1.6 5.E-03 TPD52L1 249 175 767 267 3.1 5.E-03 CDR2L 118 82 211 27 1.8 5.E-03 GPSN2 402 181 675 73 1.7 6.E-03 LAD1 209 116 506 301 2.4 6.E-03 PIAS1 57 16 81 14 1.4 6.E-03 HMGCR 112 65 232 113 2.1 7.E-03 NFIB 164 126 411 103 2.5 7.E-03 NR3C1 96 79 223 58 2.3 7.E-03 ► MAP7 68 44 203 88 3.0 7.E-03 NEDD9 34 40 77 47 2.3 8.E-03 FZD6 122 71 410 236 3.4 1.E-02 ST6GALN-AC2 284 354 763 528 2.7 1.E-02 R3HDM2 134 54 208 20 1.5 1.E-02 PRKCI 133 72 265 120 2.0 1.E-02 RHOF 87 60 169 81 1.9 1.E-02 GGH 174 79 303 141 1.7 1.E-02 ABHD4 201 41 261 65 1.3 1.E-02 CD24 685 470 2328 994 3.4 1.E-02 LMO4 247 216 484 90 2.0 2.E-02 RAB25 444 266 1235 425 2.8 2.E-02 SORT1 153 88 253 87 1.7 2.E-02 SLC16A5 45 33 80 44 1.8 2.E-02 ARHGAP8 146 95 297 98 2.0 2.E-02 PTPRK 286 145 645 293 2.3 2.E-02 ZDHHC4 140 56 240 78 1.7 2.E-02 PRKCH 86 34 167 103 2.0 2.E-02 FLJ10986 68 73 96 17 1.4 3.E-02

64 GALNT3 154 111 438 266 2.8 3.E-02 ► SYNE2 90 71 177 87 2.0 3.E-02 CREBBP 82 36 120 31 1.5 3.E-02 NFYB 42 16 60 20 1.4 3.E-02 RBM35A 289 153 704 438 2.4 3.E-02 INHBA 149 233 212 32 1.4 3.E-02 ► KIAA1598 70 58 140 80 2.0 3.E-02 NRCAM 58 74 90 42 1.6 3.E-02 KCNK1 107 71 197 103 1.8 4.E-02 GTF2I 504 268 727 151 1.4 4.E-02 LOXL1 145 193 389 502 2.7 4.E-02 ► DHX40 127 109 203 51 1.6 4.E-02 SC5DL 230 114 382 190 1.7 4.E-02 HBP1 180 86 261 66 1.5 4.E-02 ► GPRC5C 104 78 154 43 1.5 5.E-02 SPINT2 891 457 1927 542 2.2 5.E-02 FBLN5 55 16 210 260 4 5.E-02 Note: a) Genes shown in Figure 2C were listed in this table and the arrow heads indicate 40 genes (in bold) which were randomly selected for validation experiments; b) and c) Means and STDEV (standard deviation) of Affymetrix microarray signal intensity values for either 21 cancer cell lines (b) or 4 HMECs (c); d) For each gene, reduction fold of expression was calculated by dividing mean of HMECs by that of cancer lines; e)Student t-test was conducted and statistical significance was assigned if p<0.05.

65

Table S8. ChIP-qPCR of H3K27me3 in 21 breast cancer cell lines and 4 HMECs MDA- MDA- MDA- SUM MDA- MDA- SUM Gene BT- UACC- BT- HCC HCC ZR- BT- HCC MB- SK- HCC HCC HMEC- HMEC- HMEC- HMEC- MCF7 MB- T-47D MB- 159 MB- MB- Hs578T 149 symbol 474 812 20 1954 70 75-1 549 1937 134- BR-3 1500 1187 125 124 126 127 361 453 PT 468 231 PT VI MAF 39.62 11.99 19.45 1.96 0.73 0.45 4.90 14.24 24.11 19.86 39.99 14.74 25.44 15.09 16.77 37.03 3.63 0.72 5.18 14.63 37.78 0.62 0.61 0.53 3.42 SFRP1 41.39 2.21 3.50 2.25 1.13 4.44 0.63 12.62 0.32 33.66 28.04 4.77 0.96 3.29 13.87 58.33 6.56 12.91 2.06 27.80 0.60 0.36 0.13 0.26 1.11 NEDD4L 9.00 1.75 1.30 2.95 12.18 0.72 6.40 1.99 1.34 9.57 2.96 5.34 13.09 0.47 2.48 5.24 2.97 6.11 9.39 8.82 4.88 0.79 0.58 0.20 1.74 CA2 5.39 13.79 14.32 3.26 1.21 2.12 14.43 1.99 23.48 0.41 0.30 18.26 50.84 4.76 1.19 17.85 7.80 3.58 6.68 11.95 0.25 0.20 0.24 0.27 1.14 DFNA5 21.61 13.51 1.69 0.70 0.34 3.69 1.08 0.07 21.61 42.65 32.53 0.58 31.84 13.66 20.85 49.51 0.90 6.67 0.13 0.15 0.23 0.47 0.10 0.24 1.88 LOX 28.21 18.94 1.96 3.64 0.09 4.83 3.10 0.76 2.87 0.27 21.82 0.21 1.42 7.43 39.31 8.18 3.67 0.22 0.10 0.23 0.08 0.20 0.06 0.17 0.20 LPHN2 5.36 2.34 22.44 0.20 0.57 2.50 9.47 0.99 22.67 0.35 39.77 0.14 0.47 8.07 24.54 4.10 0.21 0.12 0.20 0.18 0.18 0.15 0.05 0.05 0.52 HOXA9 0.71 0.47 0.12 0.33 0.06 0.39 1.60 0.12 0.12 18.45 0.74 42.81 0.19 0.02 15.02 38.21 5.90 58.60 0.53 0.08 0.05 2.10 0.98 1.39 6.74 HOXA5 2.69 6.63 0.23 0.15 0.28 0.50 2.01 0.25 0.10 23.78 0.34 21.74 0.51 0.10 30.52 21.57 5.20 25.71 1.20 0.21 0.15 0.08 0.08 0.16 1.47 TLE4 17.72 9.26 12.61 4.23 0.38 1.79 0.52 0.86 1.41 1.23 21.19 0.09 0.54 2.22 0.96 1.27 0.20 0.27 6.56 0.14 0.10 0.41 0.13 0.21 1.52 GPRC5C 0.37 0.09 0.19 0.23 0.28 0.49 0.93 5.85 0.13 0.57 0.30 18.19 42.07 6.56 0.35 15.28 0.07 26.55 35.33 0.55 0.46 0.66 1.17 0.34 2.26 PIR 2.17 0.50 0.10 0.79 0.31 0.06 4.35 0.04 0.19 4.85 10.36 0.31 0.23 0.08 21.06 12.93 0.11 0.63 0.24 1.84 0.04 2.75 0.73 2.10 4.08 CSRP2 6.69 4.08 1.95 0.62 0.35 5.41 4.76 0.13 0.39 7.87 3.69 0.13 3.76 3.74 0.48 1.38 1.10 0.42 0.18 0.15 0.16 0.19 0.06 0.10 0.73 CTGF 10.34 6.50 1.13 0.47 0.17 0.54 1.48 0.28 0.24 10.06 5.90 0.12 0.59 1.78 44.96 0.05 5.29 0.24 0.05 0.09 0.11 0.19 0.06 0.45 0.10 PROS1 8.85 2.10 1.28 0.51 0.59 3.12 1.85 0.09 4.46 14.63 2.18 0.55 8.46 2.59 12.22 3.74 0.57 0.73 0.09 0.39 0.50 0.16 0.09 0.06 0.37 LARP6 15.25 5.55 0.59 0.76 1.28 3.19 17.79 0.24 0.16 0.18 7.31 0.13 1.00 0.19 11.50 11.10 5.76 4.94 0.27 0.09 0.17 0.17 0.03 0.31 0.08 GNAI1 5.11 13.99 10.64 0.13 0.47 2.84 5.15 0.88 1.18 3.84 15.59 0.19 33.11 6.92 2.15 17.68 1.88 0.15 0.20 0.26 0.36 0.18 0.02 0.09 0.31 LAMB1 6.76 8.92 1.54 2.86 0.78 0.20 6.58 3.00 0.45 64.81 16.04 0.78 4.59 1.63 44.17 0.37 11.01 2.11 0.33 0.11 0.36 1.40 0.40 0.80 0.74 PLEKHA5 1.76 0.28 0.32 0.40 7.38 0.60 6.07 3.21 0.12 29.71 0.55 0.31 47.36 0.90 0.41 0.44 0.75 0.71 0.07 0.14 0.22 0.10 0.02 0.04 0.05 MAOA 7.41 2.99 1.37 0.59 0.73 1.43 1.25 0.12 0.17 12.15 2.42 13.79 4.90 2.37 2.98 1.86 0.17 2.91 0.04 1.64 0.10 1.65 0.53 1.12 2.56 SMARCA1 2.24 1.08 4.25 0.25 0.40 0.39 1.21 1.86 6.26 7.02 2.97 0.97 1.90 7.45 3.71 0.27 0.66 0.35 0.46 1.25 1.27 1.88 1.08 1.44 2.37 CST6 2.74 0.98 0.16 0.36 0.14 0.24 0.38 0.08 0.07 0.23 7.30 14.64 0.24 0.07 0.14 0.14 0.09 2.34 0.08 0.09 0.84 0.32 0.05 0.41 0.87 DHX40 1.35 0.19 0.21 0.54 0.27 0.47 0.51 0.31 0.41 0.42 0.53 0.36 0.23 0.83 0.12 0.17 0.37 1.02 1.45 0.26 1.68 0.46 0.35 0.50 1.06 SYNE2 0.42 0.13 0.17 0.34 0.18 0.14 0.64 2.02 0.09 0.27 0.51 0.24 0.09 0.12 0.39 0.38 0.22 0.00 0.92 0.15 0.13 1.85 1.17 1.32 1.14 MAP7 0.55 0.05 0.18 0.35 0.23 0.18 0.34 3.85 0.11 0.13 0.13 3.78 0.51 0.12 0.23 0.10 0.05 0.17 1.71 0.94 0.14 0.19 0.01 0.03 1.10 DSC2 0.16 0.19 0.21 0.12 0.90 0.33 2.18 13.04 0.10 0.17 0.17 18.16 0.28 0.13 7.83 0.12 0.12 0.21 0.87 6.77 0.06 0.15 0.03 0.21 1.66 PLEKHA1 28.71 0.06 0.27 0.49 0.90 0.15 4.86 0.19 0.22 0.86 0.50 0.32 2.00 0.23 59.37 0.53 1.43 0.62 0.45 0.28 0.19 0.10 0.05 0.07 0.10 F2RL1 1.40 0.95 0.14 0.20 0.39 0.16 0.99 0.12 0.12 0.11 0.30 4.10 0.17 0.23 1.00 0.19 2.46 0.38 0.42 1.82 0.08 0.14 0.02 0.20 1.46

66 ETS2 1.37 0.33 0.12 0.69 0.18 0.20 0.24 0.13 0.07 0.22 0.16 0.23 0.35 0.10 0.69 0.17 0.48 32.12 0.19 0.05 0.15 0.18 0.04 0.15 0.29 BTG2 0.21 0.09 0.29 0.19 0.24 0.19 0.57 0.19 0.11 1.81 0.23 1.24 0.72 0.16 0.20 0.14 0.13 0.17 4.57 0.23 1.17 0.13 0.07 0.09 0.45 IL6R 0.96 2.15 0.37 0.32 0.12 0.30 0.27 0.22 0.13 0.42 0.15 2.44 0.70 0.42 7.41 0.08 0.30 0.10 0.55 0.39 0.24 0.13 0.07 0.18 0.32 ANKRA2 0.09 0.06 0.13 2.69 0.41 0.12 1.27 0.25 0.04 0.37 0.18 0.03 0.62 0.21 1.40 0.13 0.30 2.13 0.06 0.04 0.54 0.00 0.02 0.10 0.03 LIMK2 0.56 0.11 0.23 0.09 0.33 0.07 0.41 0.16 0.07 0.14 0.24 0.31 0.69 0.23 0.21 0.17 0.22 0.33 0.19 0.19 0.20 0.09 0.08 0.47 0.08 RGS12 0.04 0.07 0.10 0.36 0.14 0.15 0.19 0.09 0.07 0.14 0.33 0.04 0.13 0.03 0.12 0.16 0.04 0.03 0.08 0.02 0.18 0.31 0.14 0.17 0.21 KIAA1598 0.22 0.18 0.13 0.24 0.06 0.18 0.37 0.14 0.09 0.29 0.23 0.20 0.59 0.30 0.45 0.13 0.05 0.29 0.20 0.15 0.15 0.47 0.14 0.42 0.50 TNFAIP8 0.30 0.22 0.34 0.28 0.29 0.48 0.67 0.21 0.17 0.26 0.54 0.13 0.46 0.33 0.38 0.24 0.11 0.35 0.26 0.26 0.20 0.08 0.01 0.11 0.16 PAWR 0.19 0.03 0.19 0.14 0.32 0.08 0.40 0.17 0.29 0.23 0.29 0.18 0.25 0.06 0.28 0.08 0.02 0.16 0.35 0.22 0.11 0.07 0.02 0.05 0.07 AUH 0.22 0.04 0.20 0.09 0.23 0.08 0.40 0.23 0.16 0.16 0.17 0.11 0.42 0.10 0.26 0.08 0.12 0.11 0.11 0.16 0.09 0.12 0.05 0.08 0.18 CROT 0.03 0.03 0.10 0.21 0.19 0.10 0.32 0.07 0.06 12.09 0.09 0.11 0.05 0.07 0.18 0.04 0.08 0.53 0.00 0.09 0.05 0.03 0.00 0.10 0.27 KLF5 0.07 0.05 0.08 0.05 0.15 0.03 0.24 0.03 0.06 0.05 0.07 0.15 0.05 0.03 0.28 0.07 0.06 0.09 0.01 0.04 0.05 0.02 0.00 0.00 0.01

67 Table S9. meDIP-qPCR in 21 breast cancer lines, 4 HMECs, and myrAKT1- or Vector transfected MCF10A cells UAC MDA- MDA- SUM MDA MDA- MDA- SUM MCF MCF Gene BT- T- BT- HCC HCC ZR- BT- HCC SK- HCC HCC Hs HMEC HME HMEC HMEC- C- MCF7 MB- MB- 159 -MB- MB- MB- 149 10A 10A symbol 474 47D 20 1954 70 75-1 549 1937 BR-3 1500 1187 578T -96 C-97 -111 113 812 361 453 PT 468 134-VI 231 PT AKT1 Vec MAF 9.64 0.30 1.03 0.49 58.45 97.06 59.64 9.20 0.41 0.21 0.55 5.08 12.30 0.50 12.79 0.21 12.65 0.19 12.43 1.33 0.13 6.30 4.27 0.23 0.00 0.09 0.03 SFRP1 10.48 36.60 19.14 23.25 54.50 76.79 67.57 10.85 58.01 0.15 7.86 1.58 0.21 0.03 19.05 0.33 9.88 0.22 17.86 6.32 0.22 0.19 0.14 0.40 0.02 0.33 0.09 NEDD4L 6.97 7.25 5.01 9.29 50.29 79.08 25.04 6.55 12.10 10.74 8.94 35.12 8.13 10.71 5.23 12.65 12.06 12.82 7.41 3.57 6.27 10.01 9.29 2.04 4.52 3.19 4.41 CA2 8.59 1.02 0.15 1.40 47.31 61.03 2.93 5.81 6.64 0.12 2.30 5.23 4.87 0.23 0.59 1.27 1.05 0.94 0.33 2.39 0.20 0.22 0.32 0.43 0.07 0.42 0.30 DFNA5 2.34 1.56 20.67 9.44 4.12 88.46 71.21 0.94 13.99 2.03 3.98 3.77 2.23 1.10 13.58 0.37 21.19 1.99 0.64 0.39 0.37 1.95 1.76 1.02 0.37 0.61 1.25 LOX 14.30 0.46 0.39 1.31 93.71 44.35 56.62 16.81 0.13 0.12 1.08 2.20 0.39 1.13 21.78 0.09 7.25 0.26 0.23 0.03 0.03 0.89 0.28 0.55 0.00 0.07 0.45 LPHN2 9.50 3.45 8.89 3.68 60.08 35.32 30.45 2.81 2.88 3.30 2.78 6.67 2.47 3.27 10.13 1.06 4.19 4.07 2.37 1.64 1.31 3.30 2.26 0.91 0.96 0.49 0.81 HOXA9 4.40 15.58 25.67 10.41 20.69 7.02 17.68 9.68 8.70 14.46 4.29 5.88 11.11 8.99 6.44 4.23 4.49 2.81 6.30 7.43 13.12 14.41 4.95 2.41 3.00 3.01 4.14 HOXA5 0.75 0.54 0.24 4.01 3.14 100.9 58.51 0.52 22.21 2.59 6.90 1.62 0.41 0.57 9.41 9.25 6.09 3.56 5.85 0.19 0.22 0.28 0.52 0.50 0.08 0.34 0.21 TLE4 17.38 0.15 0.74 0.40 37.60 2.53 1.89 26.73 0.27 0.13 0.31 0.87 0.25 0.20 0.28 0.62 27.35 0.06 20.73 0.03 0.13 0.07 0.30 0.55 0.08 0.00 0.19 GPRC5C 3.91 1.59 0.46 1.13 7.84 1.53 2.59 6.97 0.99 1.95 0.94 19.38 6.50 1.88 0.40 0.55 0.36 9.24 0.44 5.30 0.87 2.55 0.88 0.98 0.41 0.41 0.85 PIR 1.34 10.98 0.12 10.52 1.69 0.36 16.59 0.61 10.16 1.51 1.99 0.60 0.12 0.11 3.88 0.08 0.06 0.11 0.21 5.83 0.01 0.32 0.12 0.40 0.11 0.14 0.29 CSRP2 3.06 6.86 0.54 8.97 5.03 93.27 2.89 0.81 2.14 1.30 6.51 1.88 13.58 3.36 1.14 4.09 7.10 2.75 1.44 0.15 0.52 6.55 7.97 0.23 0.11 0.79 0.47 CTGF 1.31 0.72 0.17 0.96 5.60 89.48 28.05 0.80 0.25 0.49 1.15 1.33 1.29 0.67 8.68 0.38 2.01 1.05 0.27 0.32 0.17 0.82 0.65 0.22 0.15 0.39 0.43 PROS1 2.27 0.05 0.03 0.27 15.15 0.62 24.35 0.12 0.34 0.18 0.21 0.26 0.14 0.14 5.44 0.05 0.07 0.20 0.05 0.13 0.64 0.31 0.14 0.25 0.06 0.30 0.16 LARP6 1.98 0.10 0.08 0.22 0.99 20.43 0.75 0.62 23.47 0.21 0.95 0.60 0.38 0.96 0.16 0.63 0.21 0.42 0.03 0.00 0.19 0.48 0.39 0.27 0.13 0.49 0.28 GNAI1 1.99 0.51 0.11 0.61 3.16 0.99 1.23 0.29 0.52 1.14 1.23 2.94 1.00 0.86 0.41 0.41 11.78 0.49 0.21 0.51 0.44 1.64 0.29 0.35 0.11 0.58 0.56 LAMB1 1.09 0.05 0.81 0.55 1.61 0.67 0.37 0.37 0.74 0.29 0.77 1.02 0.19 0.33 0.23 0.34 21.14 0.23 11.75 0.21 0.08 0.42 0.17 0.06 0.06 0.60 0.43 PLEKHA5 0.95 0.65 0.03 0.23 0.87 0.63 0.22 2.56 0.17 1.18 0.28 0.36 0.54 0.34 0.10 0.00 1.81 0.49 0.00 0.17 0.99 0.19 0.34 0.09 0.24 0.38 0.17 MAOA 13.40 7.94 0.24 15.81 45.83 0.83 52.56 5.00 10.15 7.94 7.31 9.07 25.23 11.14 14.64 5.62 2.14 13.69 0.35 26.63 28.67 15.55 9.21 2.38 2.99 1.40 1.50 SMARCA1 5.42 15.44 9.26 25.34 24.60 88.50 55.24 17.79 9.14 7.32 7.36 3.69 19.00 12.44 15.67 24.40 8.17 14.84 1.61 1.44 5.77 9.34 9.60 4.86 5.16 12.95 9.99 CST6 8.58 25.17 26.43 27.36 48.00 0.13 73.86 63.00 67.47 0.24 5.16 5.86 53.31 1.69 17.96 41.42 20.06 7.92 13.73 63.81 2.81 11.31 5.30 0.41 0.20 1.02 0.34 DHX40 16.89 7.23 3.38 4.74 25.10 40.93 0.00 10.42 5.65 12.21 6.68 0.04 17.48 1.27 0.04 7.60 9.40 2.37 12.12 5.81 4.62 6.65 2.58 1.24 0.05 1.49 1.58 SYNE2 8.65 1.87 0.46 1.56 13.55 7.26 4.35 2.21 1.93 0.64 3.59 4.13 11.16 3.68 3.09 1.14 2.68 0.00 0.00 1.15 1.61 5.89 2.51 0.13 0.19 0.42 0.12 MAP7 15.59 0.34 0.09 0.25 85.79 0.94 0.11 32.61 0.08 0.27 0.57 2.97 0.04 0.04 0.10 0.23 0.08 0.16 1.07 2.63 0.04 0.21 0.10 0.32 0.08 0.12 0.09 DSC2 9.70 0.45 0.50 0.52 40.80 0.57 2.80 2.83 0.31 0.30 0.95 6.02 0.11 0.29 0.33 0.20 0.29 9.83 2.07 9.62 0.22 0.63 0.29 0.36 0.13 0.50 0.37 PLEKHA1 0.42 0.11 0.01 0.07 0.66 0.00 0.05 0.05 0.10 0.14 0.34 0.21 0.00 0.06 0.01 0.11 0.06 0.17 0.08 0.00 0.06 0.09 0.09 0.47 1.00 0.13 0.18 F2RL1 1.23 0.23 0.53 0.57 1.26 0.59 12.78 76.98 0.16 0.19 0.82 0.89 0.26 0.09 6.94 0.24 0.10 0.10 0.06 0.61 0.26 0.29 0.16 0.23 0.03 0.70 0.01 ETS2 0.47 0.33 0.17 3.92 1.33 0.97 0.51 22.92 0.51 0.17 0.50 0.45 0.24 0.19 0.16 0.72 0.19 1.54 0.20 0.16 0.07 0.34 0.22 0.41 0.07 0.75 0.11 BTG2 0.85 0.15 0.13 0.23 0.17 4.00 0.31 0.49 0.19 0.08 0.25 0.95 1.48 0.07 0.06 0.70 0.14 0.04 0.00 0.03 0.19 0.07 0.37 0.37 0.13 1.41 0.24 IL6R 0.61 0.13 0.23 0.10 0.39 0.00 0.22 0.14 0.42 0.11 0.44 1.21 0.00 0.01 0.03 0.35 0.02 0.03 0.04 0.74 0.69 0.08 0.10 0.15 0.05 0.35 0.02 ANKRA2 0.94 0.34 0.11 0.51 1.83 0.34 0.46 0.28 0.14 0.55 0.65 0.91 0.11 0.40 0.13 0.10 0.11 0.30 0.25 0.08 0.13 0.59 0.34 0.21 0.13 0.25 0.36

68 LIMK2 1.89 0.33 0.71 0.96 5.48 3.45 1.14 0.93 0.08 1.37 1.03 5.13 1.41 0.46 0.34 0.73 0.27 0.82 0.75 0.29 0.24 0.59 0.93 0.72 0.40 1.22 0.58 RGS12 2.14 0.44 0.36 1.74 6.39 3.03 2.20 1.38 0.36 2.57 1.54 2.67 1.61 1.01 0.60 0.53 0.56 1.14 1.27 0.62 0.76 1.37 1.25 0.58 0.22 1.74 0.82 KIAA1598 0.70 0.10 0.05 0.18 0.30 4.76 2.43 13.27 0.25 0.07 0.19 1.86 0.38 1.81 1.02 0.31 0.11 0.76 0.61 2.92 0.59 2.12 1.32 0.31 0.06 0.22 0.12 TNFAIP8 1.50 0.26 0.26 0.22 2.59 1.92 5.53 0.28 0.28 0.45 0.80 1.15 0.44 0.66 1.90 0.86 0.22 0.39 0.27 0.35 0.20 0.45 0.33 0.26 0.17 1.14 0.42 PAWR 1.23 0.33 0.16 0.32 2.85 0.00 0.42 0.53 0.03 0.51 0.21 0.92 0.33 0.08 0.14 0.17 0.07 0.09 0.32 0.00 0.59 0.52 0.00 0.22 0.02 0.00 0.21 AUH 0.70 0.22 0.10 0.07 0.60 1.38 0.09 0.34 0.20 0.09 0.37 0.39 0.15 0.13 0.07 0.24 0.06 0.13 0.02 0.02 0.04 0.47 0.35 0.34 0.06 0.16 0.18 CROT 1.70 0.10 0.15 0.12 2.90 0.23 0.67 0.00 0.13 0.42 0.28 0.68 0.21 0.01 0.09 0.05 0.00 0.10 0.09 0.09 0.00 0.05 0.00 0.42 0.09 0.97 0.27 KLF5 0.48 0.19 0.12 0.31 0.58 0.00 0.00 0.17 0.15 0.25 0.31 1.29 0.08 0.28 0.06 0.18 0.05 0.31 0.02 0.13 0.16 0.32 0.14 0.10 0.02 0.10 0.20

69 a Table S10. PCR primers of 40 genes Name Forward Reverse ANKRA2 GCCAGAAGGCGAAAGAAGAA GACGACAGCAGACAGCGAGT AUH1 GTCCACGCCGTAAACAGACA AGAGCCACGCACTGCAAG BTG2 AGGGTAACGCTGTCTTGTGGAC CTTAAGCCTCTGCTCGCTCAC CA2 GAGGCCACTGTGGAGGAATC CCTCCTCCTAGGTCCGGTTA CROT AAGACGCCCACTGGAGACAG GTGCGGGAATTGGACTGAAG CSRP2 AGCTGGAAATCGGACGAGAG GGGAGGCTCCAGCAGTAGAA CST6 GGAGAACTCCGGGACCTGT TGTGCGTGTCTCGGAAGTAG CTGF ATGCGAGGAATGTCCCTGTT GCACTGGCTGTCTCCTCTCA DFNA5 TCCGGATCCTCTTTGGTCTG GGGATGCTGACTGCGAGTT DHX40 GGCAGAATAGCCTGCAGAGA GCCCTGATGACGTAGAGGTG DSC2 TTGTGCAGTCAGGGCTTCTG CTGCGCAAGGTGTTTCTCAC ETS2 GGCTCAATTTCAGGGCCTTAT CTAACGCCAAACCTGCCTTT F2RL1 GTACGCTGCTCCTTCGGTTT GGACGCACCGAGAGAAAGTC GNAI1 CGGCCACTGTACCCAGAGAT CTAAGCGGAGTCGAGGGAGA GPRC5C GAGTCAGAGCCAACGTGTCC GACCTCCACCAGTCACCAAG HOXA5 ACTCTCCTCAGCCCGATCC CCCTCTCTGCTGCTGATGTG HOXA9 CTCACACTTTGTCCCTGACTGACT GGATTTGAAGGGAGGAGACACTTA IL6R AGCGCGAGTTCCTCAAATGT TCTCTACACACACTGCGAGTCC KIAA1598 CCAGAGTCTACTGCGGGAAA CGTGTGTGGGAACTCCACTT KLF5 CTGCCTCTCTCCCTGCTCAT CCGCCTCTATTTCACCCAAC LAMB1 GCAGATTCGGCTTTCAAACA AGCCTTGGGAGGAACAGAGG LARP6 CCGGAGTCAAGCACAAACAG CGATCACTCCCTCCGTCTTT LIMK2 CCAGGTGTGGTTTGGTCCTC GGAGATAACAGCGGGACAGG LOX TTCCTGCGCTCAGTAACCTG CCACGTCGAGAAGCCACATA LPHN2 GTGCATGTGTGTGGACAGGA CACACCCATTCAACCGCTAA MAF GCTGGTGACCATGTCTGTGC CTCTGCTGCACCCTCTTGAA MAOA GCTCCCGGAGTATCAGCAAA GGGTGGGAAGGACCCTTCTAT MAP7 CCCATGTACTTCGCCTCTCC CGCTATTTCCCTCCGAACTC NEDD4L GACGGCGCTAGCGAGGAG GGAAGGCTGCGGGACCAG PAWR GATACGACGAGCCGACAGGT CCACCCTGCAAAGTTTCTCC PIR ACAGCAAGTGCCGCCTAAAT TCGGGAATGTCACTCCACTC PLEKHA1 GGCATCCTTTCCTGGTGTTT GAAGGTGCGGAGGTAAATCG PLEKHA5 GGGCATTATTAGGCTCCCTTT GAAGGTTCCGGGATCGATTA PROS1 GCTTCGAAATGAGGGTCCTG CGCAGTTCAGTCGACAATGC RGS12 CCAGCGGAGGCAGAGAAA GGGAAGCAGGGATGAGAAGA SFRP1 TGAGCTTCCAGTCGGACATC GGGCAGCACCATCTTCTTGT SMARCA1 CTCCACCTTCCCGGAACTC GGATTGAAGGGCCCAGATTT SYNE2 GATCCGGACCACACTACGAA TGGTGTGAGGGAGAGACCAC TLE4 GCGACTCCATTTCTGGCTCT AAGCTCGGCCTTGTGTAACG TNFAIP8 AGTGTGAGTGGGTGCGTTTG GGGTCTTGGATCCTCAGTGC Note: a) PCR primers (total 40 pairs) in table were used in both ChIP-qPCR and meDIP-qPCR.

70 Table S11. Gene expression after drug treatment DAC TSA DAC+TSA PI3Ki DAC+TSA+PI3Ki Gene Symbol BT- MDA- ZR- BT- MDA- ZR- BT- MDA- ZR- BT- MDA- ZR- BT- MDA- ZR- 549 MB-468 75-1 549 MB-468 75-1 549 MB-468 75-1 549 MB-468 75-1 549 MB-468 75-1 MAF 3.89 1.08 0.76 5.03 1.97 30.48 8.46 1.47 28.05 0.21 2.06 2.91 4.11 0.38 119.43 SFRP1 0.88 0.56 1.55 0.66 0.77 N.D. 0.81 0.71 1.28 2.01 1.84 1.12 1.21 2.35 11.24 NEDD4L 0.99 1.34 0.64 0.64 0.79 2.11 0.52 0.31 1.69 0.71 0.66 0.85 0.91 0.88 1.96 CA2 1.97 1.33 0.53 1.16 1.55 0.56 0.92 1.53 0.58 0.75 1.97 0.55 0.87 2.13 0.53 DFNA5 1.16 0.72 0.84 0.65 0.66 1.39 0.68 0.48 2.53 2.11 1.69 0.41 1.75 2.20 3.10 LPHN2 1.44 1.28 1.27 2.68 0.66 1.82 1.73 0.36 2.83 1.59 1.07 0.63 3.20 0.44 6.92 HOXA5 0.65 0.99 0.49 0.80 0.96 0.71 0.34 0.62 0.98 0.12 0.99 0.62 1.23 1.40 0.84 HOXA9 0.45 0.75 1.16 1.15 1.20 2.97 1.89 1.37 2.48 3.10 1.27 1.72 1.27 3.29 4.59 LOX 0.93 1.16 0.43 1.04 0.55 0.90 0.72 0.62 1.18 1.08 0.55 0.04 0.45 0.32 1.78 TLE4 1.10 1.10 16.4 2.35 1.09 150.1 1.42 0.72 116.16 0.47 1.56 13.93 1.29 1.77 639.15 GPRC5C 1.02 2.46 0.62 2.27 0.49 4.99 1.55 0.41 1.87 1.06 0.60 1.92 7.46 0.65 1.20 PIR 0.93 0.95 0.77 1.35 0.90 1.72 0.87 0.62 1.46 0.68 0.53 0.56 0.99 0.58 0.96 CSRP2 1.23 0.96 1.34 0.66 0.74 0.31 0.84 0.76 0.58 0.86 0.91 0.89 1.01 0.88 2.77 CTGF 0.95 1.93 1.93 1.39 3.76 6.54 0.89 4.53 13.55 2.10 8.94 1.61 1.10 16.80 53.08 PROS1 1.03 1.59 0.52 1.67 0.86 4.17 1.21 4.00 4.53 1.21 1.21 0.00 1.92 4.76 2.35 LARP6 1.26 1.29 1.27 0.42 1.34 1.14 1.27 1.47 1.91 1.09 1.84 0.78 1.68 2.57 11.16 GNAI1 1.51 1.11 0.88 1.40 0.86 1.57 1.80 1.33 1.79 1.18 1.69 1.23 1.96 0.67 1.25 LAMB1 0.78 1.35 0.64 1.34 0.45 5.06 1.10 0.70 2.41 4.66 0.66 1.46 3.53 2.03 2.13 PLEKHA5 1.52 0.60 0.62 1.36 0.46 0.31 0.99 0.48 0.55 0.71 0.81 0.61 1.71 0.23 0.98 MAOA 3.61 24.25 1.48 2.50 18.77 7.01 4.08 15.14 6.50 9.32 15.45 0.85 23.26 27.67 3.92 SMARCA1 1.64 0.72 1.39 1.55 0.40 0.63 1.61 0.62 1.06 1.62 0.74 1.12 2.11 0.15 1.54 CST6 2.08 0.84 1.44 12.13 1.56 1.15 17.63 2.17 1.40 3.53 0.56 0.27 29.86 1.65 0.78 DHX40 1.13 0.74 0.99 1.88 0.55 1.27 1.66 0.64 1.73 1.64 1.04 0.90 2.81 0.41 3.56 SYNE2 1.75 0.64 0.48 2.46 0.26 0.39 1.08 0.27 0.45 2.69 0.92 1.01 4.53 0.33 0.49 MAP7 2.06 1.53 0.75 5.50 1.06 4.41 6.68 0.70 3.71 1.65 1.40 1.21 17.88 1.59 1.69 DSC2 1.30 0.92 0.78 0.74 0.67 0.94 0.66 0.44 2.00 1.30 1.01 0.75 0.68 0.54 1.09 PLEKHA1 1.28 0.48 0.99 1.29 0.44 0.47 1.09 0.52 0.94 0.81 0.54 0.80 1.71 0.13 1.59 F2RL1 1.95 0.84 0.66 4.63 0.64 0.69 4.69 0.33 0.92 1.85 0.99 0.46 7.94 0.77 1.87 ETS2 1.23 1.73 0.66 0.55 1.21 2.66 0.58 0.53 2.22 1.16 1.52 1.04 1.06 2.48 0.86 BTG2 0.86 4.14 0.78 0.38 1.92 7.52 0.40 1.56 3.86 1.22 2.39 1.27 0.88 8.94 2.10 IL-6R 24.59 1.01 4.59 21.86 1.16 28.25 9.65 0.71 3.39 2.06 1.15 4.59 3.61 1.72 5.86 ANKRA2 1.33 1.12 0.59 2.00 1.06 1.17 1.36 1.19 1.17 1.72 1.45 1.06 2.99 0.99 1.21 LIMK2 0.92 1.85 0.86 1.15 1.26 4.08 0.72 0.85 2.38 1.87 1.55 0.86 2.64 3.43 2.13 RGS12 1.93 3.36 0.38 2.35 0.66 6.50 1.88 1.62 2.14 3.46 0.39 1.83 8.00 6.06 1.56

71 KIAA1598 1.66 0.74 0.55 0.68 0.46 2.38 0.97 0.34 3.16 1.28 1.26 1.25 0.77 0.40 1.91 TNFAIP8 1.09 0.68 N.D. 0.73 0.60 0.01 0.77 0.44 1.06 1.04 0.78 1.65 0.76 0.20 0.54 PAWR 1.20 0.74 1.46 1.42 0.89 2.27 1.21 1.21 2.33 2.10 1.23 1.89 3.16 1.01 6.28 AUH 1.15 0.63 1.35 0.65 0.64 0.78 1.42 1.22 1.35 1.09 0.85 1.01 1.73 0.58 3.97 CROT 1.27 0.89 1.16 1.38 1.01 2.85 1.55 1.11 2.97 0.99 1.11 2.06 1.27 0.98 2.50 KLF5 1.42 1.04 0.83 1.36 1.24 1.56 1.31 1.39 2.75 1.80 1.39 1.55 2.43 0.91 2.71

Table S11. cont’d DAC TSA DAC+TSA PI3Ki DAC+TSA+PI3Ki Gene T- HCC BT- MCF T- HCC BT- T- HCC BT- T- HCC BT- T- HCC BT- MCF Symbol MCF7 MCF7 MCF7 47D 1954 474 7 47D 1954 474 47D 1954 474 47D 1954 474 47D 1954 474 7 MAF 1.06 2.11 1.06 1.30 3.14 0.98 0.62 0.53 4.23 1.33 0.44 12.73 1.80 1.51 0.81 2.58 1.35 0.69 1.26 15.67 SFRP1 N.D. 3.27 N.D. N.D. N.D. N.D. N.D. N.D. N.D. N.D. N.D. 0.29 N.D. N.D. N.D. N.D. N.D. 0.65 N.D. 1.68 NEDD4L 0.40 0.39 0.98 1.67 0.44 0.54 0.85 1.96 0.23 0.48 0.44 0.70 0.26 0.73 1.73 3.47 0.24 1.21 1.69 3.39 CA2 N.D. 0.18 1.27 1.22 N.D. 0.30 0.64 0.56 N.D. 0.79 0.43 25.99 N.D. N.D. 0.28 4.86 N.D. 0.78 0.21 19.29 DFNA5 0.75 1.53 1.05 1.20 1.09 0.69 0.38 0.97 0.99 1.60 2.55 1.08 0.71 1.13 0.41 1.79 1.54 3.68 1.49 0.67 LPHN2 N.D. 0.87 1.03 5.47 1.16 1.95 0.54 1.85 1.44 2.77 0.27 8.04 0.55 0.52 1.79 71.69 N.D. 1.99 0.85 N.D. HOXA5 0.58 0.67 1.41 2.28 1.09 0.84 0.33 1.27 0.80 0.97 0.80 0.59 0.93 1.51 3.58 6.68 1.48 2.50 0.43 2.82 HOXA9 0.79 0.19 2.07 1.41 0.62 0.46 3.18 3.16 0.54 0.62 3.58 0.44 0.45 0.39 4.92 2.68 1.80 1.14 0.12 11.1 LOX 0.17 1.73 1.62 0.77 0.20 0.61 0.53 0.86 1.85 0.98 0.72 1.46 0.01 2.73 0.77 0.63 0.38 1.72 0.44 0.97 TLE4 0.07 0.66 2.58 4.66 0.25 0.96 1.27 20.0 0.15 1.31 1.54 243.88 0.06 1.36 0.74 237.2 0.16 4.41 1.06 600.5 GPRC5C 0.44 0.09 1.44 0.95 0.81 0.45 0.62 1.15 0.42 0.47 0.34 1.09 0.35 0.10 2.04 1.29 0.85 0.61 0.74 3.53 PIR 0.47 0.67 1.20 1.04 0.55 0.87 0.71 0.57 0.36 0.82 0.70 0.45 0.38 0.38 0.69 0.36 0.54 1.07 1.56 0.55 CSRP2 1.60 1.11 1.43 0.65 1.11 1.21 0.23 0.32 1.29 1.15 0.37 0.71 0.70 1.20 0.95 1.06 1.96 1.45 0.73 1.01 CTGF 2.31 2.50 3.81 0.34 2.17 0.93 1.36 0.43 3.14 1.31 2.33 12.04 0.97 1.15 0.94 9.13 2.64 3.10 6.02 17.0 PROS1 0.86 0.95 1.89 1.45 0.99 2.75 4.08 0.88 0.91 3.36 4.14 0.79 0.31 0.90 1.10 1.59 0.44 6.50 29.7 1.28 LARP6 0.90 1.62 1.72 1.93 1.19 1.43 0.61 0.71 1.02 1.58 0.63 1.02 1.16 1.84 0.81 5.98 1.65 2.79 1.25 4.66 GNAI1 1.01 1.40 1.21 1.44 1.84 1.37 0.76 0.75 1.31 1.51 0.48 1.87 1.32 1.92 0.54 2.62 1.01 2.33 0.66 0.55 LAMB1 0.81 0.19 2.08 0.77 0.77 0.53 1.21 0.96 0.66 0.71 1.14 0.91 0.41 0.34 3.16 3.19 0.95 3.36 1.73 2.33 PLEKHA5 0.82 0.88 0.88 0.77 0.79 0.72 0.63 0.81 0.59 0.65 0.45 1.39 0.65 1.16 1.37 2.64 0.51 1.66 1.26 0.60 MAOA 0.51 0.55 2.14 2.27 2.41 0.89 1.13 2.33 0.09 1.04 0.54 0.72 1.85 0.76 6.41 2.15 3.32 1.19 1.75 4.69 SMARCA1 1.47 1.71 1.77 0.86 0.81 0.81 0.59 0.39 0.98 1.91 0.72 1.35 1.04 2.35 1.56 2.16 0.95 3.20 1.59 0.25 CST6 36.0 2.06 3.92 2.51 2.03 1.35 0.77 0.73 18.4 2.10 5.50 3.21 0.75 0.72 1.31 1.03 24.4 2.79 4.03 2.05

72 DHX40 0.77 0.99 0.91 0.76 0.87 1.09 0.85 0.73 0.88 1.29 0.67 1.44 0.88 1.66 1.58 3.40 1.39 3.18 2.13 0.63 SYNE2 0.52 0.51 0.65 0.98 1.01 0.69 0.57 1.19 0.68 0.80 0.31 0.74 0.71 1.74 2.58 3.68 0.51 2.95 1.40 0.31 MAP7 0.47 0.44 1.69 1.83 1.26 0.84 1.35 1.05 0.59 1.04 0.91 0.30 0.70 1.04 2.60 2.00 0.63 2.50 3.43 1.33 DSC2 N.D. 0.73 1.80 2.02 N.D. 1.00 1.04 1.93 N.D. 1.13 0.93 1.74 N.D. 1.96 2.11 1.24 N.D. 2.23 2.45 1.75 PLEKHA1 1.08 0.99 0.98 0.83 0.97 1.65 0.19 0.57 1.01 1.19 0.50 1.45 0.65 1.66 1.33 1.23 0.87 2.41 1.46 0.18 F2RL1 0.76 0.74 1.42 2.42 1.20 0.85 0.58 1.77 1.24 1.00 0.64 0.82 0.68 0.80 1.45 2.28 1.29 1.74 2.08 2.69 ETS2 0.41 0.37 1.49 2.74 0.97 0.54 0.95 2.81 0.63 0.59 0.79 0.54 0.33 0.57 1.51 1.97 0.49 1.01 1.55 4.08 BTG2 0.78 0.21 1.72 3.01 1.10 0.44 1.38 2.66 0.49 0.48 0.97 1.03 0.28 0.51 5.10 6.72 0.76 1.34 4.29 18.4 IL-6R 0.54 0.20 1.16 1.74 2.87 0.25 0.50 1.38 1.84 0.28 0.49 0.92 0.75 0.20 0.32 0.13 1.68 0.72 0.57 11.6 ANKRA2 1.05 2.23 1.19 0.97 1.04 1.38 1.01 0.29 1.05 1.33 0.63 10.13 1.35 1.28 1.20 4.59 1.10 2.14 1.31 1.15 LIMK2 0.84 0.24 1.27 1.36 1.92 0.64 0.77 1.45 0.60 0.62 0.70 0.43 0.68 0.53 2.81 2.69 1.75 2.55 1.97 3.84 RGS12 0.90 1.32 1.31 0.73 0.77 1.21 0.95 0.61 0.54 0.91 0.81 0.76 0.45 2.99 3.12 4.66 1.44 5.74 2.39 2.05 KIAA1598 0.45 0.64 0.64 1.04 0.82 0.66 0.88 1.09 0.61 0.87 0.52 0.70 0.85 1.11 1.53 3.79 0.65 1.45 1.58 0.36 TNFAIP8 0.72 0.66 1.12 1.20 1.06 0.94 0.02 1.07 1.04 1.05 2.60 2.11 0.97 0.90 1.26 1.24 0.85 1.26 3.34 0.59 PAWR 0.78 0.67 1.07 0.85 1.13 1.04 0.84 0.85 0.86 0.91 0.76 1.19 1.06 1.58 1.62 1.91 1.59 2.30 2.71 0.68 AUH 1.14 0.58 0.54 0.39 0.80 0.91 0.81 0.37 0.78 0.55 0.59 1.10 0.82 1.46 0.73 1.60 2.13 1.19 1.42 1.46 CROT 0.93 1.01 1.06 1.52 1.84 1.37 1.13 1.18 1.42 0.96 0.68 5.78 1.24 2.39 0.79 9.00 1.11 2.91 1.39 2.13 KLF5 1.01 0.37 1.09 0.96 1.71 1.38 0.93 0.43 1.35 1.38 0.68 11.88 1.51 1.87 1.01 6.50 1.20 2.64 0.95 1.48

Table S11. cont’d DAC TSA DAC+TSA PI3Ki DAC+TSA+PI3Ki Gene MDA- MDA- MDA- MDA- MDA- MDA- MDA- MDA- MDA- MDA- Symbol MB- Hs578T MB- MB- Hs578T MB- MB- Hs578T MB- MB- Hs578T MB- Hs578T MB-453 MB-231 453 231 453 231 453 231 453 231 MAF 0.99 0.63 2.08 1.60 0.50 2.01 1.65 0.98 5.82 0.32 0.67 6.59 16.00 2.95 1.79 SFRP1 0.37 0.74 8.63 0.03 1.18 N.D. 0.91 1.27 4.41 N.D. 0.71 N.D. N.D. 0.93 N.D. NEDD4L 0.78 0.72 1.42 2.36 1.16 0.97 3.16 0.61 0.55 0.93 0.47 0.84 6.54 0.65 0.66 CA2 0.82 3.01 1.21 0.29 1.59 0.56 0.29 3.81 2.28 0.22 1.06 0.86 0.58 9.71 1.42 DFNA5 2.20 0.82 1.17 3.39 0.79 0.78 3.39 0.97 0.90 0.13 1.55 1.16 1.83 1.89 1.69 LPHN2 0.92 0.91 1.64 0.99 1.92 0.91 2.22 1.60 0.68 0.80 0.64 2.77 1.24 1.37 1.22 HOXA5 1.49 0.77 0.99 3.32 1.54 1.36 10.20 1.02 1.09 4.82 1.16 1.00 142.02 1.01 4.06 HOXA9 2.33 1.22 0.59 8.63 2.14 1.34 13.09 1.83 1.09 13.93 1.65 1.03 171.25 2.10 3.10 LOX 0.59 0.92 2.20 1.46 0.82 2.38 0.01 1.07 2.60 0.03 0.91 1.10 N.D. 1.89 2.58 TLE4 0.78 1.02 0.68 2.45 1.00 1.2 1.82 1.01 2.48 2.51 1.00 0.37 5.70 3.66 1.74

73 GPRC5C 1.64 2.57 1.67 1.27 3.01 1.06 2.19 0.90 1.10 0.81 0.71 0.84 8.28 0.48 0.98 PIR 0.87 0.93 1.53 0.93 1.40 2.08 0.77 1.06 1.79 0.41 0.45 0.72 0.84 0.62 1.54 CSRP2 1.44 1.39 1.24 1.36 0.77 1.03 3.20 0.78 1.23 0.66 0.81 0.97 7.78 1.13 2.20 CTGF 0.84 0.66 0.79 2.73 0.61 0.66 2.43 0.74 1.52 0.13 1.79 1.08 9.25 4.66 1.92 PROS1 1.15 0.76 1.27 1.19 0.69 0.58 2.57 0.85 0.75 0.86 0.38 0.75 N.D. 0.44 1.20 LARP6 0.80 0.74 0.86 0.24 0.69 0.91 0.98 0.84 1.41 0.26 0.69 0.85 20.68 2.53 1.44 GNAI1 0.81 0.77 1.36 1.78 0.85 1.39 1.41 0.86 2.20 0.83 0.56 1.04 2.68 1.87 1.60 LAMB1 1.19 1.09 0.90 2.87 1.09 1.48 10.06 1.12 0.93 2.13 0.76 1.01 5.17 0.78 0.82 PLEKHA5 0.62 1.02 0.81 0.82 0.70 0.93 1.27 0.62 0.62 0.98 0.43 0.84 2.45 0.42 0.86 MAOA 1.56 0.81 2.66 0.67 2.06 0.85 10.13 2.20 0.75 3.89 1.64 2.81 75.58 1.29 1.79 SMARCA1 2.75 1.11 1.03 1.71 0.62 0.97 17.63 0.93 0.84 1.85 0.78 0.76 52.71 1.80 1.15 CST6 1.99 7.26 1.06 2.50 1.20 1.29 4.86 5.50 2.33 0.99 2.19 0.58 26.54 9.51 5.58 DHX40 0.98 0.84 1.09 1.28 0.69 0.89 1.80 0.88 0.84 1.26 0.91 0.97 3.58 1.47 1.65 SYNE2 0.79 0.85 0.70 0.85 1.40 0.98 1.64 1.13 0.72 0.97 0.68 2.43 2.01 2.28 1.55 MAP7 1.07 1.39 1.79 1.51 2.06 1.62 2.01 2.36 1.21 1.93 1.73 1.97 3.68 4.86 3.05 DSC2 1.23 1.09 0.85 0.86 1.28 0.40 2.93 1.41 0.57 1.51 0.66 0.67 2.25 1.40 0.50 PLEKHA1 0.88 1.04 0.83 1.16 0.42 1.16 1.23 0.64 1.32 0.88 0.53 0.67 1.47 1.07 2.10 F2RL1 0.97 0.75 1.38 0.55 1.17 0.73 0.78 1.23 0.72 0.69 0.41 1.55 2.14 0.91 0.85 ETS2 1.65 1.28 1.82 3.73 2.39 0.95 4.82 1.68 0.88 2.16 1.43 1.60 4.29 1.80 1.39 BTG2 1.24 1.60 2.69 3.97 3.36 1.52 4.72 1.79 4.59 2.43 1.57 4.17 20.11 1.92 5.78 IL-6R 1.56 0.96 2.13 0.48 0.37 1.12 4.59 0.89 0.99 1.54 0.74 5.31 1.49 3.12 11.63 ANKRA2 0.97 0.72 1.00 2.03 0.58 0.76 1.64 0.89 1.80 1.14 1.08 1.45 8.88 3.61 2.41 LIMK2 1.82 1.27 2.13 4.72 2.16 1.58 5.35 1.27 0.73 2.87 1.24 1.35 12.64 0.93 1.12 RGS12 0.60 0.78 1.47 3.76 1.13 4.20 8.17 0.61 0.81 2.14 1.87 2.30 31.78 2.53 1.82 KIAA1598 0.68 0.88 0.84 1.45 1.28 0.79 2.17 1.22 0.69 1.01 0.79 1.42 2.07 1.60 0.74 TNFAIP8 0.46 0.76 1.27 N.D. 0.83 0.73 3082.7 0.85 1.04 N.D. 0.31 0.49 10587 0.42 0.93 PAWR 1.25 1.58 0.87 1.93 1.27 0.81 2.77 1.28 0.90 2.97 2.06 1.79 5.28 5.46 3.18 AUH 1.37 1.33 0.44 1.97 0.52 0.51 2.50 0.70 0.49 2.81 0.96 0.43 6.45 1.42 1.93 CROT 0.95 0.86 0.89 4.23 0.45 1.06 3.16 0.99 1.88 1.01 0.39 0.88 10.27 1.79 1.56 KLF5 1.21 0.84 1.21 2.79 0.72 0.59 2.69 1.03 1.23 0.67 0.82 1.23 17.39 2.99 1.35 Note: a) Gene expression values in each treatment were determined by normalization to those in DMSO control. N.D. stands for not detected.

74 a Table S12. RT-PCR primers of 40 genes Name Forward Reverse ANKRA2 AGCAAATTCTTTGTCTGTTCACCAG AGAGGAGTAAATCCTTCTTCATCCG AUH1 AGGAGGAGAACCGAGGAATTGT CAGATTTCAAAGCATCCACAGC BTG2 ACTTCCCACCCGAGACCTCTCA TAAGCCTCTGCTCGCTCACGCA CA2 TTTGTTCACAGCATGTAGGGTGAT GCCTTAACTAGCTCAATTTATCTTG CROT ACAGACTTCATGGACACCCTGG GGCACCACCTCACTGCTTCAAC CSRP2 GCTCCCGCCTCCGACTCAAAAT AAAGCAGCAGCGGTGGAAGCTC CST6 GACTGCCGCAAGACC GAAGTGCCCTCCACCA CTGF CCCAGTGACAGCTAGGATGTGC CCAGTCTAATCGACAGGATTCCGA DFNA5 AGGAGCTTAGAGTGGAGTTTACAGGA TCAACCAGGAAAGTCCAAGGC DHX40 TCCCCCTCCCCTTGCTACAA AAACCGGGACATAGACCTGGCC DSC2 TGCTGACCCTCGCGATCTTA GCAGCTGTAAAGCACTCTTTCAG ETS2 GCAGCGGCAGGATGAATGA AGGTGTCAAAGGCTGGCTGG F2RL1 ACGCTGCTCCTTCGGTTT TGGACGCACCGAGAGAAA GNAI1 GCTCAGAGCAACCTCCAGCCTT TGTTGTCCAACCAGCCCAGG GPRC5C CTGGAACGGTCACAGGAAACC CTCCACCAGTCACCAAGCGTAC HOXA5 GTGCTATAGACGCACAAACGACCGC TCCGGGCCATTTGGATAGCG HOXA9 CCTGGGCAACTACTACGTGGAC AAGCTGCACGGGCTGAAGTC IL6R GGTGACAGAGCAAGTGAGACCC CCCTAGAGTAGAGAAGAGGCAGGCT KIAA1598 GAGTAGGTGCGTGGGGATGA AAAGCAAGATGCCGGTGG KLF5 TGTTCAGTAAACAAATCAGTTGGCA TGTTCAATGGCTATTTGTGAATTGC LAMB1 GGCGTCTTCTCCACTCCTCT TGAACTCGGGTTCCTGAGC LARP6 AAAGCTGTCCTGATTGGTATGAAGC AAGCTCCTCGACTCTCTTGTTCAG LIMK2 GCTGGCGGGTGAAGATGTCT AAGAGCCGTGCCAGGTTT LOX CCGTTGCCTTCCAGGACTGA AAGCAATGCCAAGGGTGG LPHN2 CGGCGAACAGACGTTCTTTCT CCCGTCTCCAGGTTTTCTCTTTT MAF CAAGTTGGAGCCATCAGTGGG GGTGGTTCTCCATGACTGCAAAT MAOA GCGCTCCCGGAGTATCAGCAAA ACAGGAGTGGGGACGGCAAA MAP7 GCAGTGCGAAGCGAAACA GGTCTGGTTTATTTCCTGAGTGG NEDD4L TATGGACTTTCCGAAGACGAGGG TCTCATCCGCTACGTACAATGAAAG PAWR ATCCAGGCAGTTCCTATCTGCT CTGAAACATTTGCATCCCTGTT PIR GCTGAGTCACGGTGAGGCTA AGGTACTCACGCTGCGGTA PLEKHA1 TTTGGTGCAGTTTAGCATGTTCC CGAAGAAATTTCCCACTGTTTTCAT PLEKHA5 GGCGGCTAGGGATCAGACAT TTGGCCTCCTCGTTGATGAAG PROS1 CGCGCTTCGAAATGAGGGT GCTTCCTAACCAGGACTTGTGA RGS12 TTTACTAAGTACGCATGTTCTGTGTCC CCAGCAATAGGATCATAAACAGATTTG SFRP1 TCGGCCAGCGAGTACGACTA TTCTTGTAGCCCACGTTGTGG SMARCA1 CTAGCTCTTTCCAGTGCAGCC TTTCTTCATGCGGGGTTTGTC SYNE2 TGGAATCTTTAGAGACAGCACTGCG GGTGTTGATAGATGCGATCAGCA TLE4 TTGGCTGCTTTCTTCCCC GAAACGCTTGCGGCTTTT TNFAIP8 ACTCTTGCAGAACTTTCCCC CGCACACGACGGAAAATA Note: a) RT-PCR primers (total 40 pairs) were used for measuring expressions of 40 genes in cancer cells after drug treatments.

75 Table S13. MassARRAY PCR primers of 4 genes Name Forward Reverse HOXA5 GATGGGTAGATTGTTTTTAGGGTTT CAAAAAACATATACTATTTCAATCCTCC HOXA9 GGGGATTTTGGGTTAGTTTTT AAAACAATCACCCCTTCTAACC SFRP1 TGGGTTATAAGAAGATGGTGTTGTT CAACCTTACCTTAAAACTTAAAAACTTC SYNE2 TTATTTAAGGGGAAGGAGGAATTTA AATAAACAAAAACCACAAACTCCCT

a Table S14. Summary of MBDCap-seq data DMSO DAC LY DAC + LY Raw reads 43,275,135 56,886,494 47,819,151 45,761,730 Mapped reads 37,543,090 50,501,066 39,407,563 34,943,682 Unique mapped reads 26,119,748 35,913,287 27,010,543 24,748,988 Note: a) MBDCap-Seq analysis is described in Experimental procedures.

Table S15. Differentially methylated genes (n=143) identified by MBDCap-seq analysis.

Gene Cancer Accession chr. Strand Region start Region end a symbol Related MEAF6 NM_022756 chr1 - 37750951 37754951 CLCC1 NM_001048210 chr1 - 109305634 109309634 SYPL2 NM_001040709 chr1 + 109808622 109812622 RAP1A NM_001010935 chr1 + 111961927 111965927 ZNF697 NM_001080470 chr1 - 119989913 119993913 HAX1 NM_001018837 chr1 + 152509662 152513662 DYRK3 NM_001004023 chr1 + 204873503 204877503 PARP1 NM_001618 chr1 - 224660424 224664424 Yes SFRS7 NM_001031684 chr2 - 38830140 38834140 C2orf86 NM_015910 chr2 - 63667355 63671355 KIAA1310 NM_001115016 chr2 - 96665842 96669842 LOC91149 NR_026995 chr2 - 173307180 173311180 GPR155 NM_001033045 chr2 - 175058057 175062057 ICA1L NM_138468 chr2 - 203442616 203446616 NR2C2 NM_003298 chr3 + 14962239 14966239 SS18L2 NM_016305 chr3 + 42605301 42609301 TMEM158 NM_015444 chr3 - 45240818 45244818 ZNF717 NM_001128223 chr3 - 75914945 75918945 COMMD2 NM_016094 chr3 - 150950968 150954968 KLHL24 NM_017644 chr3 + 184834104 184838104 TNK2 NM_001010938 chr3 - 197104829 197108829 Yes LMLN NM_001136049 chr3 + 199169467 199173467 ARAP2 NM_015230 chr4 - 35920374 35924374 CTSO NM_001334 chr4 - 157092498 157096498 SCAMP1 NM_004866 chr5 + 77690094 77694094 GIN1 NM_017676 chr5 - 102481741 102485741

76 MEGF10 NM_032446 chr5 + 126652354 126656354 ISOC1 NM_016048 chr5 + 128456340 128460340 TXNDC15 NM_024715 chr5 + 134235358 134239358 HSPA9 NM_004134 chr5 - 137937014 137941014 YIPF5 NM_001024947 chr5 - 143528471 143532471 SH3RF2 NM_152550 chr5 + 145294318 145298318 C6orf129 NM_138493 chr6 - 37573678 37577678 C6orf108 NM_006443 chr6 - 43303189 43307189 ZNF451 NM_001031623 chr6 + 57060786 57064786 ICA1 NM_004968 chr7 - 8266710 8270710 TMEM196 NM_152774 chr7 - 19776929 19780929 KIAA0895 NM_015314 chr7 - 36371375 36375375 MRPS17 NM_015969 chr7 + 55985104 55989104 DNAJC30 NM_032317 chr7 - 72733717 72737717 WBSCR27 NM_152559 chr7 - 72892791 72896791 PDK4 NM_002612 chr7 - 95061861 95065861 PTCD1 NM_015545 chr7 - 98872355 98876355 RABL5 NM_001130820 chr7 - 100749813 100753813 SRPK2 NM_182692 chr7 - 104814577 104818577 KRBA1 NM_032534 chr7 + 149041080 149045080 NEIL2 NM_001135746 chr8 + 11662580 11666580 ZDHHC2 NM_016353 chr8 + 17056206 17060206 EPB49 NM_001114136 chr8 + 21966273 21970273 KIAA0146 NM_001080394 chr8 + 48334094 48338094 MED30 NM_080651 chr8 + 118600145 118604145 GCNT1 NM_001097633 chr9 + 78261887 78265887 SECISBP2 NM_024077 chr9 + 91121231 91125231 C9orf129 NM_001098808 chr9 - 95146517 95150517 TSC1 NM_000368 chr9 - 134807841 134811841 Yes TMEM141 NM_032928 chr9 + 138803597 138807597 SUV39H2 NM_024670 chr10 + 14958904 14962904 PDSS1 NM_014317 chr10 + 27024600 27028600 EPC1 NM_025209 chr10 - 32674119 32678119 ZNF239 NM_001099282 chr10 - 43388071 43392071 C10orf53 NM_001042427 chr10 + 50555689 50559689 NT5C2 NM_001134373 chr10 - 104941046 104945046 CARS NM_001014437 chr11 - 3033247 3037247 TAF10 NM_006284 chr11 - 6588021 6592021 IPO7 NM_006391 chr11 + 9360744 9364744 MAPK8IP1 NM_005456 chr11 + 45861777 45865777 KLC2 NM_001134775 chr11 + 65779666 65783666 TPCN2 NM_139075 chr11 + 68570925 68574925 POLD3 NM_006591 chr11 + 73979276 73983276 PAK1 NM_001128620 chr11 - 76860756 76864756 PRSS23 NM_007173 chr11 + 86187138 86191138 CWC15 NM_016403 chr11 - 94344424 94348424 LOH12CR2 NR_024061 chr12 - 12399268 12403268 PYROXD1 NM_024854 chr12 + 21479804 21483804 ZNF641 NM_152320 chr12 - 47028268 47032268 SARNP NR_026722 chr12 - 54495807 54499807 RAB21 NM_014999 chr12 + 70432924 70436924 WDR51B NM_172240 chr12 - 88441908 88445908 APPL2 NM_018171 chr12 - 104152138 104156138 RBM19 NM_001146699 chr12 - 112886559 112890559

77 RNF34 NM_025126 chr12 + 120320284 120324284 TMEM120B NM_001080825 chr12 + 120633040 120637040 FAM124A NM_145019 chr13 + 50692507 50696507 GPR180 NM_180989 chr13 + 94050104 94054104 METT11D1 NM_001029991 chr14 + 20525804 20529804 C14orf138 NM_001040662 chr14 - 49651047 49655047 HIF1A NM_001530 chr14 + 61229871 61233871 Yes FLJ43390 NR_015358 chr14 + 61651827 61655827 ACOT2 NM_006821 chr14 + 73103524 73107524 MTMR15 NM_001146095 chr15 + 28981346 28985346 TP53BP1 NM_001141979 chr15 - 41570646 41574646 Yes C15orf48 NM_032413 chr15 + 43508054 43512054 HMG20A NM_018200 chr15 + 75498297 75502297 IREB2 NM_004136 chr15 + 76515572 76519572 FAM108C1 NM_021214 chr15 + 78772706 78776706 AP3S2 NM_005829 chr15 - 88236621 88240621 UNC45A NM_001039675 chr15 + 89272413 89276413 PGP NM_001042371 chr16 - 2202823 2206823 MAGMAS NM_016069 chr16 - 4339301 4343301 DEXI NM_014015 chr16 - 10941758 10945758 SCNN1B NM_000336 chr16 + 23219091 23223091 RRN3P2 NR_003369 chr16 + 28991663 28995663 SEPHS2 NM_012248 chr16 - 30362725 30366725 TMEM188 NM_153261 chr16 + 48614689 48618689 MT1DP NR_027781 chr16 + 55233216 55237216 KATNB1 NM_005886 chr16 + 56325160 56329160 GLG1 NM_001145666 chr16 - 73196543 73200543 DYNLRB2 NM_130897 chr16 + 79130354 79134354 KLHDC4 NM_017566 chr16 - 86355043 86359043 PRDM7 NM_001098173 chr16 - 88667839 88671839 FAM57A NM_024792 chr17 + 580596 584596 YBX2 NM_015982 chr17 - 7136600 7140600 C17orf44 NR_026951 chr17 - 8066086 8070086 HS3ST3B1 NM_006041 chr17 + 14143230 14147230 C17orf63 NM_001077498 chr17 - 24191967 24195967 G6PC3 NM_138387 chr17 + 39501623 39505623 PSMC5 NM_002805 chr17 + 59256763 59260763 CCDC46 NM_145036 chr17 - 61616449 61620449 GGA3 NM_014001 chr17 - 70767272 70771272 FLJ35220 NM_001164638 chr17 + 76001563 76005563 FN3KRP NM_024619 chr17 + 78265870 78269870 RNF165 NM_152470 chr18 + 42166184 42170184 ELAC1 NM_018696 chr18 + 46746384 46750384 ANGPTL4 NM_001039667 chr19 + 8333010 8337010 PPAN NM_020230 chr19 + 10075964 10079964 FARSA NM_004461 chr19 - 12903558 12907558 ETV2 NM_014209 chr19 + 40822486 40826486 EIF3K NM_013234 chr19 + 43799561 43803561 C19orf47 NM_178830 chr19 - 45544133 45548133 ZNF581 NM_016535 chr19 + 60844797 60848797 ZNF773 NM_198542 chr19 + 62701120 62705120 TRIB3 NM_021158 chr20 + 307307 311307 NOP56 NM_006392 chr20 + 2579253 2583253 NCOA5 NM_020967 chr20 - 44149987 44153987

78 UBE2V1 NM_001032288 chr20 - 48161117 48165117 SH3BGR NM_001001713 chr21 + 39737666 39741666 PWP2 NM_005049 chr21 + 44349635 44353635 FLJ39582 NR_027052 chr22 + 19684404 19688404 ZMAT5 NM_001003692 chr22 - 28490969 28494969 HMOX1 NM_002133 chr22 + 34105086 34109086 Yes WBP2NL NM_152613 chr22 + 40722674 40726674 ACOT9 NM_001033583 chrX - 23669328 23673328 RAB9B NM_016370 chrX - 102971868 102975868 a) 6 genes were shown to associate with cancer by functional analysis conducted by IPA (Ingenuity Pathway Analysis) software, and method of pathway analysis was described in experimental procedures.

Experimental procedures:

ChIP-seq Data Analysis

All ChIP-seq samples were initially sequenced to generate a set of raw reads

(each read has a length of 36 bp DNA fragment). A total of 15.6 and 11.8 million reads in AKT and vector transfected MCF10A, respectively, were mapped to unique genomic locations using the UCSC human assembly hg18. Subsequently, bin-base enrichment thresholds (BELT) algorithm (Frietze et al., 2010; Cited in main text) was employed to call peaks (binding sites). Briefly, BELT program starts to determine the enrichment value of each level of the top percentile from all enriched regions. Then number of the peaks at each level of the top percentile was consequently identified by the program. The significant enrichment at each percentile was determined by randomly permutation-based statistical method.

False discovery rate (FDR) was assigned to be less than 0.05 in order to determine peaks at the top 1%, 2%, and 10% illustrated in Table S 1 and S2.

Functional Pathway Analysis

IPA (Ingenuity Pathway Analysis, http://www.ingenuity.com) software was used to conduct computational analysis on PI3K/AKT- downstream genes identified by

ChIP-seq and gene expression microarray assays. The list of interesting genes

79 was uploaded to program for statistical calculations. Briefly, Fisher Exact Test was performed to determine p value which indicates the likelihood that a particular function or pathway is associated with the set of genes analyzed. As a result, the more interesting genes in data set are found in a particular diseases or cellular functions, the more likely the association with this biological function is real, and thereby the p-value would be more significant.

Reference:

Saal, L. H., Gruvberger-Saal, S. K., Persson, C., Lovgren, K., Jumppanen, M., Staaf, J., Jonsson, G., Pires, M. M., Maurer, M., Holm, K., et al. (2008). Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair. Nat. Genet. 40, 102-107.

Stemke-Hale, K., Gonzalez-Angulo, A. M., Lluch, A., Neve, R. M., Kuo, W. L., Davies, M., Carey, M., Hu, Z., Guan, Y., Sahin, A., et al. (2008). An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res. 68, 6084-6091.

80