Supplementary Information

Supplementary Materials and Methods

Multiple myeloma specimens

Primary bone marrow samples from 116 MM patients and 12 patients without tumors

were obtained from the 4th Department of Internal Medicine, Hiroshima Atomic-Bomb

Survivors Hospital; the 1st Department of Internal Medicine, Sapporo Medical

University Hospital; and the Department of Hematology, Teine Keijinkai Hospital after

acquisition of informed consent from each patient. Mononuclear cells were separated

from 99 samples using Ficoll-Paque (StemCell Technologies), after which we separated

the CD138-positive cells using CD138 MicroBeads (Miltenyi Biotec). There were five

patients whose bone marrow specimens were collected before and after treatment. All

five of those patients received treatment with Dex. Of those five patients, three

received bortezomib and Dex; one received vincristine, adriamysin and Dex; and one

received melphalan and Dex followed by peripheral blood stem cell transplantation.

Methylation analysis

Combined bisulfite restriction analysis (COBRA) were performed as described

previously (1). The PCR products were digested with the restriction endonuclease Hinf

(TaKaRa) and precipitated with ethanol, after which the resultant DNA fragments were

subjected to 2.5% agarose gel electrophoresis and stained with ethidium bromide.

Bisulfite-pyrosequencing was carried out as described previously (2). The primers

used for COBRA were also used for pyrosequencing. After PCR, the biotinylated

PCR product was purified, made single-stranded, and used as a template in the

pyrosequencing reaction. Briefly, the PCR products were bound to streptavidin

sepharose beads HP (Amersham Biosciences), after which beads containing the

immobilized PCR product were purified, washed, and denatured using a 0.2 mol/L

NaOH solution. After addition of 0.3 μmol/L sequencing primer to the purified PCR

product, pyrosequencing was carried out using a PSQ96MA system (Biotage) and Pyro

Q-CpG software (Biotage). MM-related genes were deemed methylated if the level of

methylation was above the 75th percentile level found in control bone marrow samples.

Statistics

Paired t tests were used to compare differences in methylation levels before and after

treatments. Pearson’s and Spearman’s correlation coefficients (r and rs, respectively)

were calculated to evaluate the correlation between gene expression levels

(log-transformed), fold expression levels, and methylation levels. Cell viability was

assessed using one way ANOVA with post hoc Dunnett’s test. All statistical

calculations were performed using SPSSJ 15.0 (SPSS Japan Inc.).

References.

1. Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay.

Nucleic Acids Res 1997; 25: 2532-4. 2. Yang AS, Estecio MR, Doshi K, Kondo Y, Tajara EH, Issa JP. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 2004; 32: e38.

Legends for Supplementary Figures.

Supplementary Figure 1.

Representative results of real-time PCR analysis of genes upregulated by DAC in MM

cell lines. Expression levels of CST1 and IER3 relative to that in normal bone marrow

are shown on the Y-axis.

Supplementary Figure 2.

Expression profile of candidate genes silenced by DNA methylation in MM. The heat

map shows the expression profiles in normal colon, normal stomach and three cancer

cell lines. Levels of expression are normalized to that in normal bone marrow.

Supplementary Figure 3.

Representative results of real-time PCR of candidate methylation target genes in MM

cell lines treated with DAC.

Supplementary Figure 4.

Summary of gene expression in MM cells treated with DAC. Levels of expression are

normalized to those in mock treated cells.

Supplementary Figure 5.

Bisulfite-sequencing analysis of BNIP3 and SOCS3 in MM cell lines. Open circles

indicate the unmethylated CpG sites; filled circles indicate the methylated CpG sites.

Supplementary Table 1. Primer sequences and restriction enzymes used in this study.

Primer

Gene name Forward Reverse Restriction enzymes

COBRA

GPR30 GGTYGAGTGTTTTTGGAGGT CCTTTATCCRCTAAATATAAATAATAC TaqI

FMR1NB GTTAYGGATTGTTTTGGAAG TTACCAACTCTAAATAAACCACAC MboI

CST6 TTYGAGTTTYGTTTTAGTTTTAGGT TAACAACRCCAAAAAACAAAATAC HhaI

TNFRSF4 TAYGGTGTTTAGTTTTAGGTTTAGGAGATCCCCRACCTACCACCTTC TaqI

SECTM1 GGAGTTTTAGGAAAATGAAAG CCCRTAAAAATAATAAATTCAC HhaI

PTRF AGYGGGAGATTYGGAGAGAAGT CCTCCCTTTCTAAAATAAAACCAACC TaqI

C16orf30 TTTTTGTTGAGAGTTAGGGAAG ACACCRACCTACTATAAATACCA MboI

RASD1 GTTTTTAGTTTTAGTTYGATTTTGGA CCRCCCTTATATACAACCTACTC AfaI

DAZL TGAAGAGAAAAGGAAAATTAAGAG AAACRCTACCACCCATTAAC TaqI

DDX43 TAATGGTTGYGTGAAATTAGTG CCTCCRTAATAAAACATTATTCC MluI

PDIA2 GGTTTTGTTTTTGTTGGGATTG AAATTTCCTCCTCTAAAAACTCCTC MluI

FES TTYGGGGTTTGGGTTAATTG ACRCCTACTCTACCCCTACCTAC TaqI

COX7A1 GTTTTAGTTTYGTYGYGTTTTTAG AACCCAACCCATAAAAACCTCA TaiI

KRTCAP3 GGGGTYGGGTTTAGGTATAG CACRAAAAAAAACAAAATTAAATC HhaI

RRAD TTGAGAAGGYGGTGGTTGTAGTAGTACCRAAACCCCTCCRAACCTAA TaqI

FGFR3 GGGGTYGGGAYGTAGGAGT RCAAACAAAAACRCCCATAAC TaqI

IER3 GYGTTTAGGATTGTGTATGTTAAGT TAAACCRAACRAAATATAAAACCA TaqI

TKTL1 ATATTTTAGATTTTTTGATTTGTTTG TTAAAATCTAAAAACCCACTCCT TaqI

CMTM3 GGTGGTTAAGAAAGTYGTAAGAAA CCACCCRTCTACCCCTATC MluI

SYT11 GYGGAGTTTATTTTTTATTAGGA CTCTAAAAACCCTCRATCAATAC MboI

P2RY6 GGATTTTAGYGGTGYGGAG CAACTAATCCRACCCAAATATCACT TaiI

GDF15 TTTAGAGTYGTAATTTGTATAGTTATGTCRAAATACAACTCTAAAAATCC TaqI

RASD1 pyro-seq1GYGTTTAGAGAGTAGGAGTT

Bisulfite-sequencing

BNIP3 GATATGGYGTTAGAGGGTAATTG CCCRCCCTACCCTATAAATTC

SOCS3 GTTTTTTTTTGTTGYGAGTAGTGAT CRTCCCTCRAACTTCCCCT

ABL1 TTGGTTYGGGTTGGTTTTGGAAAG AAACCRAAACCCCTCTCCCAACTC

Y=C or T, R=G or A

12/26/20083:09 AM

Supplementary Table 2. Genes up-rehulated by DAC in KMS12PE.Gene Name Systematic Name DACVIM NM_003380 181.2TNFRSF4 NM_003327 113.0GPR30 NM_001505 85.6VASN NM_138440 78.6CST6 NM_001323 63.7FMR1NB NM_152578 46.1CKM NM_001824 45.1AIF1 NM_004847 44.5COX7A2 NM_001865 44.0CMTM3 NM_144601 38.5GPR68 NM_003485 35.9VIM NM_003380 35.3LOC645277 XM_928321 32.0RAB13 NM_002870 31.7TAS1R1 NM_138697 31.2EDNRB NM_003991 30.4B3GALT4 NM_003782 28.9CXCL9 NM_002416 28.5PLAT NM_000930 27.5CCRL2 NM_003965 27.5TNFAIP2 NM_006291 27.4ACRC NM_052957 26.1LAG3 NM_002286 25.8A_24_P177634 A_24_P177634 24.6C16orf30 NM_024600 24.4THC2333719 THC2333719 23.7MYO1G NM_033054 23.1ID2 NM_002166 22.8M32220 M32220 22.7P2RY5 NM_005767 22.5SECTM1 NM_003004 20.7GPX1 NM_201397 20.6IFI27 NM_005532 19.8CCR9 NM_006641 19.4PEPP-2 NM_032498 18.9ART3 NM_001179 18.8

IFI27 NM_005532 18.1ENST00000371388 ENST00000371388 18.0APOE NM_000041 17.6PTRF NM_012232 17.4CHRDL2 NM_015424 17.4CLDN19 NM_148960 17.3HAS3 NM_005329 17.0EPHA2 NM_004431 17.0THC2337710 THC2337710 17.0LGALS8 NM_006499 16.9SPINT1 NM_003710 16.5IFI27 NM_005532 16.5ZP1 NM_207341 16.3LOC440335 BC022385 16.2THC2373524 THC2373524 15.7AGMAT NM_024758 15.6CDKN1C NM_000076 15.3TNF NM_000594 15.1CYB5R2 NM_016229 15.0IFI27 NM_005532 14.9IFI27 NM_005532 14.8IFI27 NM_005532 14.8IFI27 NM_005532 13.8BTBD14A NM_144653 13.8CCR7 NM_001838 13.5TMEM49 BC024020 13.5AGXT2L1 NM_031279 13.4ANGPT2 NM_001147 13.4IFI27 NM_005532 13.4NGB NM_021257 13.2CNDP1 NM_032649 13.1IFI27 NM_005532 13.1AHNAK NM_001620 13.1RAMP1 NM_005855 13.0BM045853 BM045853 12.9ICOS NM_012092 12.8RUNX3 NM_004350 12.6LXN NM_020169 12.2

SYT11 NM_152280 12.2RPGRIP1 NM_020366 12.2IFI27 NM_005532 12.2TNNC2 NM_003279 12.1FLJ25410 NM_144605 11.9GLULD1 NM_016571 11.9MET NM_000245 11.8PROC NM_000312 11.7A_24_P478940 A_24_P478940 11.3ENST00000381781 ENST00000381781 11.2GPR56 NM_201525 11.0SPINT2 NM_021102 11.0GNG11 NM_004126 11.0PLXND1 NM_015103 11.0BC036938 BC036938 10.9RASD1 NM_016084 10.9FARP1 NM_005766 10.8P2RY6 NM_176798 10.7LEFTY1 NM_020997 10.6CD52 NM_001803 10.6GDF15 NM_004864 10.5A_24_P109661 A_24_P109661 10.4A_23_P15226 A_23_P15226 10.4ENST00000320378 ENST00000320378 10.3VCX2 NM_016378 10.2WBP5 NM_016303 10.2KITLG NM_000899 10.1RHBDL3 NM_138328 10.0THC2383841 THC2383841 10.0

Supplementary Table 3. Genes up-regulated by DAC in RPMI8226.Gene Name Systematic Name DACGPR30 NM_001505 217.7FMR1NB NM_152578 191.1DAZL NM_001351 187.0DDX43 NM_018665 185.0BC036938 BC036938 121.7GSTP1 NM_000852 110.9CST6 NM_001323 89.8THC2376729 THC2376729 77.7VCX3A NM_016379 76.9VCX NM_013452 72.5VCX2 NM_016378 72.4THC2407823 THC2407823 67.8SYCP3 NM_153694 64.5NEFH NM_021076 62.6PAGE2 NM_207339 61.7VASN NM_138440 58.8CXCL9 NM_002416 57.5TNFRSF4 NM_003327 57.0PRAME NM_206956 55.4PDIA2 NM_006849 54.0CKM NM_001824 51.4PAGE5 NM_130467 49.2DAZ2 NM_001005785 45.5A_24_P7750 A_24_P7750 44.5XIST NR_001564 41.3UCHL1 NM_004181 39.3BM668321 BM668321 38.2ENST00000370363 ENST00000370363 38.2CNDP1 NM_032649 37.6ECAT8 AK023134 37.2LEFTY1 NM_020997 36.9ENST00000311695 ENST00000311695 36.6MXRA8 NM_032348 35.6TAS1R1 NM_138697 34.6RTP3 NM_031440 34.5BEX1 NM_018476 33.2

CARD9 NM_052813 32.0KRT19 NM_002276 31.8LGALS2 NM_006498 31.7IL18 NM_001562 31.6FES NM_002005 30.7RAB7B NM_177403 30.2CD52 NM_001803 29.9CPLX3 NM_001030005 29.6AIF1 NM_004847 28.7P2RY5 NM_005767 27.8A_23_P15226 A_23_P15226 27.6VCY NM_004679 27.6SECTM1 NM_003004 27.2ART3 NM_001179 27.0FAM26A NM_182494 26.9CDH1 NM_004360 26.3THC2304038 THC2304038 25.1LAG3 NM_002286 24.8CYB5R2 NM_016229 24.3COX7A1 NM_001864 24.2CNN3 NM_001839 24.2GPR68 NM_003485 23.9VCX2 NM_016378 23.0THC2437822 THC2437822 22.4THC2333719 THC2333719 22.2LY6K NM_017527 22.1C8G NM_000606 21.9LOC643431 XM_928128 21.0DMRTB1 NM_033067 20.8A_32_P112546 A_32_P112546 20.7CGREF1 NM_006569 20.0CCRL2 NM_003965 19.7PPAPDC3 NM_032728 19.3A_24_P401124 A_24_P401124 19.3ACRC NM_052957 18.5MYO1G NM_033054 18.4RRP22 NM_001007279 18.3RP13-36C9.6 NM_001007551 18.2

DNALI1 NM_003462 17.9HORMAD1 NM_032132 17.9HSD17B1 NM_000413 17.7CATSPER1 NM_053054 17.6FLJ10324 NM_018059 17.5CRYAA NM_000394 17.4TEKT2 NM_014466 17.2APOC1 NM_001645 16.9PKP3 NM_007183 16.8A_24_P745352 A_24_P745352 16.8PTRF NM_012232 16.5KRTCAP3 AY358993 16.4MAEL NM_032858 16.3CRYBA4 NM_001886 16.2RAMP1 NM_005855 16.1NDRG4 NM_022910 15.9ENST00000353250 ENST00000353250 15.8SMARCA1 NM_003069 15.6A_24_P195974 A_24_P195974 15.4RP4-742C19.3 NM_181773 15.4RGS1 NM_002922 15.3FAM9C NM_174901 15.0BCNP1 NM_173544 15.0SERPINF1 NM_002615 14.6RAB13 NM_002870 14.5MMP13 NM_002427 14.2PTGER1 NM_000955 14.1C6orf154 NM_001012974 14.0S100A16 NM_080388 13.8RRAD NM_004165 13.7KRTCAP3 NM_173853 13.7C16orf30 NM_024600 13.6CR613736 CR613736 13.6DNMT3L NM_013369 13.4A_24_P93111 A_24_P93111 13.2RAB34 NM_031934 12.8LOC285401 AK091178 12.7LTK NM_002344 12.7

FGFR3 NM_000142 12.6TMEM49 BC024020 12.6RARRES2 NM_002889 12.6RRAD NM_004165 12.6IER3 NM_003897 12.4BCL2A1 NM_004049 12.3ROBO3 NM_022370 12.3BEX2 NM_032621 12.3RBMY1B NM_001006121 12.2EDG6 NM_003775 12.2A_24_P341546 A_24_P341546 12.2TKTL1 NM_012253 12.1CLIC3 NM_004669 12.0FAM9C NM_174901 11.9KRT8 NM_002273 11.8PIWIL2 NM_018068 11.7THC2312585 THC2312585 11.7ZNF502 NM_033210 11.5TNF NM_000594 11.4C21orf105 BC005107 11.3ALDOB NM_000035 11.3A_24_P281605 A_24_P281605 11.2A_24_P418216 A_24_P418216 11.2A_24_P844100 A_24_P844100 11.1HSPA1A NM_005345 11.1ATP4B NM_000705 11.0ADAM8 NM_001109 10.9COL8A2 NM_005202 10.9MTMR11 NM_181873 10.8CXCL1 NM_001511 10.8ENST00000267857 ENST00000267857 10.6CLDN4 NM_001305 10.5LOC400751 BC031250 10.5HSD11B1 NM_181755 10.4SPOCK2 NM_014767 10.3CRYAA NM_000394 10.2RAB25 NM_020387 10.2FRG2 NM_001005217 10.2

EMILIN2 NM_032048 10.2THC2414226 THC2414226 10.1FBLIM1 NM_017556 10.1KRT8 NM_002273 10.1

Supplementary Table 4. Genes up-regulated by DAC and/or Dex in OPM1.Gene Name Systematic Name Dex DAC Dex+DACSSTR2 NM_001050 1.1 1.5 15.0THC2656116 THC2656116 1.1 1.1 15.0MAP9 NM_001039580 1.1 1.3 14.6ADAMTS12 NM_030955 1.1 1.1 14.3NEFL NM_006158 1.1 1.1 14.0BNIP3 NM_004052 1.9 2.1 14.0PPP1R2P9 NR_002191 1.1 1.3 13.8CXCL13 NM_006419 1.4 1.1 13.8CX3CL1 NM_002996 1.1 1.1 13.7KIAA2022 NM_001008537 1.1 1.1 13.2PARP12 NM_022750 1.1 1.1 12.8CHST2 NM_004267 1.7 1.7 12.5MLLT4 BC014505 2.0 1.2 12.3THC2660651 THC2660651 1.1 1.1 12.1RNF43 NM_017763 1.1 1.5 12.1AQP9 NM_020980 1.1 1.1 11.9CYR61 NM_001554 1.1 1.4 11.5VCAM1 NM_001078 1.1 1.1 11.0THC2668815 THC2668815 1.1 1.1 10.9BAIAP2L2 AK026235 1.1 1.2 10.9RAB31 NM_006868 1.1 1.1 10.7PCSK9 NM_174936 1.1 1.4 10.6CD109 NM_133493 1.1 1.4 10.5TRAM1L1 NM_152402 1.1 1.5 10.3AY358804 AY358804 1.1 1.1 10.3THC2662240 THC2662240 1.1 1.4 10.2LOC387763 ENST00000339446 1.3 1.6 10.2LOC441052 AF131741 1.1 1.1 10.1CMTM3 NM_144601 1.1 1.1 10.0NLRP7 NM_139176 1.1 1.1 9.9LILRB2 NM_005874 1.1 1.1 9.9TMEM16A NM_018043 1.1 1.1 9.8GNA12 NM_007353 1.6 1.6 9.8PRRX2 NM_016307 1.1 1.1 9.8CAPSL NM_144647 1.1 1.1 9.6FILIP1L NM_182909 1.1 1.1 9.6

PSG3 NM_021016 1.1 1.1 9.6BEX1 NM_018476 1.1 1.1 9.5KIF26B NM_018012 1.1 1.5 9.4TDRD6 NM_001010870 1.1 1.1 9.4MYH6 NM_002471 1.1 1.1 9.0DB090170 DB090170 1.1 1.2 8.9REN NM_000537 1.1 1.1 8.8AK001829 AK001829 1.1 1.1 8.7INSAF S73205 1.1 1.1 8.6CLDN19 NM_148960 1.1 1.3 8.5IGFL2 NM_001002915 2.5 1.7 8.4ARHGAP24 AK130576 1.9 1.6 8.3AK096803 AK096803 1.1 1.1 8.2AIF1 NM_004847 0.9 1.0 8.2SLC35D2 NM_007001 1.7 1.1 8.1SPIN3 NM_001010862 1.1 1.5 8.1TMEM45A NM_018004 1.1 1.1 8.0ZNF643 NM_023070 2.3 1.7 8.0DLK1 NM_003836 1.1 1.1 7.8HNRNPG-T NM_014469 1.0 1.3 7.8MAP9 NM_001039580 2.0 0.9 7.8C1orf115 NM_024709 1.3 1.2 7.7BMPER NM_133468 1.1 1.1 7.7MYF6 NM_002469 1.1 1.1 7.7AF090944 AF090944 1.2 1.3 7.6DLEC1 NM_007335 1.1 1.4 7.6ENO2 NM_001975 1.1 1.1 7.5RAB6IP1 NM_015213 1.1 1.1 7.5KCNS1 NM_002251 1.3 1.5 7.5BCL7A NM_020993 1.1 1.2 7.4BU624603 BU624603 2.7 1.6 7.4FN1 NM_212482 1.1 1.1 7.3DMKN NM_033317 1.1 1.1 7.2FLRT3 NM_198391 1.1 1.1 7.2MYO7A NM_000260 0.9 0.8 7.1ATP1A4 AK098076 1.1 1.1 7.1FGFBP2 NM_031950 1.1 1.4 7.1LOC400794 BC020945 1.1 1.1 7.0

ENST00000359743 ENST00000359743 1.3 1.1 7.0RETN NM_020415 1.1 1.4 7.0S100A14 NM_020672 1.1 1.1 7.0C20orf186 NM_182519 0.8 1.0 6.9EFEMP1 NM_004105 1.1 1.1 6.9DENND2C CR749576 1.2 1.1 6.8ALOX5 NM_000698 1.1 1.3 6.8LGALS8 NM_006499 1.1 1.1 6.7THC2676504 THC2676504 1.4 1.1 6.6AI859463 AI859463 1.5 1.0 6.6CYP4B1 NM_000779 1.1 1.2 6.6RAB31 NM_006868 1.1 1.1 6.6SEPT10 NM_144710 1.1 1.1 6.5MPN2 NM_183062 1.7 1.1 6.4BC037919 BC037919 1.6 1.1 6.4KIF7 NM_198525 1.1 1.1 6.4CTSL2 NM_001333 1.1 1.1 6.4RTP3 NM_031440 1.1 1.1 6.4ELL3 NM_025165 1.1 1.2 6.3A_24_P500186 A_24_P500186 1.1 1.1 6.2APOC4 NM_001646 1.1 1.3 6.2ZNF480 NM_144684 1.1 1.1 6.2PPM1J NM_005167 1.1 1.4 6.2CRISP2 NM_003296 1.1 1.1 6.2HERC5 NM_016323 1.1 1.1 6.2NUDT10 NM_153183 1.1 1.3 6.2A_23_P11119 A_23_P11119 1.1 1.3 6.2BCL2L10 NM_020396 1.1 1.3 6.1NAP1L5 NM_153757 1.1 1.1 6.0PDLIM3 NM_014476 1.1 1.1 6.0STAR NM_000349 1.1 1.1 6.0A_32_P159528 A_32_P159528 1.1 1.1 6.0KLHL5 NM_015990 1.1 1.4 6.0TTC28 AK092338 1.0 0.9 6.0ATP9A NM_006045 1.1 1.1 5.9ROS1 NM_002944 1.1 1.1 5.9KRT18P40 XR_017288 1.1 1.1 5.9THC2754547 THC2754547 1.1 1.3 5.9

FLJ40473 AK097792 1.2 1.1 5.8ADAMTS7 AF140675 1.1 1.1 5.8LOC730704 XM_001128267 1.1 1.4 5.8FHOD3 NM_025135 0.9 0.8 5.7PHLDA2 NM_003311 1.1 1.2 5.7PCDH7 NM_002589 1.1 1.1 5.6BC034306 BC034306 1.1 1.1 5.6AF118069 AF118069 1.1 1.1 5.6NEU4 NM_080741 1.5 1.1 5.6SERPINB3 NM_006919 1.1 1.1 5.6GPX2 NM_002083 1.0 1.1 5.6C6orf10 NM_006781 1.0 0.9 5.6PCDH12 NM_016580 1.1 1.1 5.6THC2728570 THC2728570 1.1 1.5 5.5COL20A1 NM_020882 1.1 1.1 5.5UNC45B NM_173167 1.1 1.4 5.5DMD NM_004019 1.1 1.1 5.5AF130074 AF130074 1.1 1.1 5.5NDN NM_002487 1.1 1.1 5.4CPVL NM_031311 1.4 1.1 5.4DLX4 NM_138281 1.1 1.1 5.4THC2535767 THC2535767 1.5 1.0 5.4TSPAN6 NM_003270 1.1 1.1 5.4ALX4 NM_021926 1.1 1.1 5.4ZFP2 NM_030613 1.1 1.2 5.4G0S2 NM_015714 1.1 1.1 5.4THC2641484 THC2641484 1.0 1.6 5.3EID3 NM_001008394 0.9 1.2 5.3A_24_P878376 A_24_P878376 1.1 1.5 5.3ID4 NM_001546 1.1 1.1 5.3FMN2 NM_020066 1.1 1.8 5.3SLC16A5 NM_004695 1.1 1.1 5.3THC2753798 THC2753798 1.1 1.9 5.3PTPN20B NM_015605 1.1 1.1 5.3DNAJB8 NM_153330 1.1 1.1 5.2PAPSS2 NM_001015880 1.1 1.9 5.2PDGFA NM_002607 1.1 1.6 5.2LAD1 NM_005558 1.1 1.5 5.2

FLJ39609 AK096928 1.1 1.1 5.2PTN NM_002825 1.1 1.9 5.2KCNIP3 NM_013434 1.1 1.1 5.2A_24_P654255 A_24_P654255 1.1 1.1 5.1HSD3B1 NM_000862 1.3 1.1 5.1KIAA1466 AB040899 1.1 1.8 5.1LOC349196 AK090418 1.0 2.9 5.1THC2616992 THC2616992 1.1 1.1 5.1DKFZP686A01247 NM_014988 1.1 1.2 5.1PDCL2 NM_152401 1.1 1.4 5.1SLC2A2 NM_000340 1.1 1.1 5.0CYP2C9 NM_000771 1.1 1.3 5.0ELF5 NM_198381 1.1 1.1 5.0PHC2 NM_198040 1.1 1.1 5.0NXPH3 AB032985 1.1 1.1 5.0DNAJA4 NM_018602 1.1 1.5 5.0LEPREL1 NM_018192 1.1 1.1 5.0USHBP1 NM_031941 1.1 1.4 5.0IRX2 ENST00000302057 1.1 1.5 5.0FAM9C BX648919 1.3 1.2 5.0A_32_P149625 A_32_P149625 0.8 1.1 5.0SORBS2 NM_021069 1.1 1.1 5.0A_24_P941450 A_24_P941450 1.1 1.1 5.0RPESP NM_153225 1.5 0.8 5.0MAK NM_005906 1.2 1.9 5.0THC2573284 THC2573284 1.1 1.2 5.0CD19 NM_001770 1.1 1.2 4.9NPY NM_000905 1.0 1.6 4.9PAQR5 NM_017705 0.9 1.3 4.9AW971282 AW971282 1.1 1.1 4.9CDH19 NM_021153 1.1 1.5 4.9ENST00000379528 ENST00000379528 1.1 1.1 4.9A_24_P736853 A_24_P736853 1.1 1.1 4.9THC2651178 THC2651178 1.0 3.0 4.9THC2661012 THC2661012 1.1 1.6 4.9COLQ NM_080542 1.1 1.8 4.9DNAJA4 AF116663 1.1 1.1 4.9CMBL NM_138809 1.0 2.8 4.8

C10orf47 NM_153256 0.9 2.6 4.8SEPSECS NM_153825 1.1 2.0 4.8BC065757 BC065757 1.1 2.0 4.8THC2716178 THC2716178 1.1 1.1 4.8FAM92A3 BC059396 1.1 1.9 4.8ENST00000370378 ENST00000370378 1.1 1.3 4.8THC2669541 THC2669541 1.1 1.1 4.8ZNF750 NM_024702 1.5 1.1 4.7THC2608967 THC2608967 1.1 1.1 4.7AA514833 AA514833 1.1 1.1 4.7DQ168992 DQ168992 1.1 1.1 4.7KIAA1279 NM_015634 2.2 1.1 4.7FLJ13231 NM_023073 1.0 2.8 4.7PENK NM_006211 0.9 0.8 4.7EIF5A2 NM_020390 1.0 2.9 4.7OR7E91P NR_002185 1.0 3.1 4.7FBP2 NM_003837 1.1 1.2 4.7NPTX1 NM_002522 1.1 1.7 4.7TCL6 NM_020552 1.1 1.8 4.7C9orf70 BC007366 1.1 1.1 4.7PROS1 NM_000313 1.1 1.9 4.7A_24_P636974 A_24_P636974 0.9 2.7 4.7BC029602 BC029602 1.1 1.1 4.7IL7R NM_002185 2.1 1.2 4.6CRB1 NM_201253 1.1 1.4 4.6RAPGEF2 AL117397 1.2 1.4 4.6CCL25 NM_005624 0.7 1.6 4.6C18orf2 AF295728 1.1 1.4 4.6DB295730 DB295730 1.1 1.1 4.6FLJ30679 AK055241 1.1 1.1 4.6THC2614840 THC2614840 1.4 1.3 4.6ARNTL2 AF256215 1.1 1.1 4.6ENST00000374860 ENST00000374860 1.0 2.9 4.6TEX14 NM_198393 1.3 1.5 4.6BC038719 BC038719 1.1 1.1 4.6THC2637155 THC2637155 1.3 1.4 4.6BC032041 BC032041 1.1 1.1 4.6FLJ22536 AK022865 0.9 2.7 4.6

C1QTNF3 AK094895 1.1 1.9 4.6MARK1 NM_018650 1.2 1.8 4.6TMEM185B NR_000034 1.1 1.6 4.6APOBEC2 NM_006789 1.1 1.1 4.5RP5-821D11.2 NM_152513 1.1 1.1 4.5TRPM4 NM_017636 1.1 1.8 4.5HGFAC NM_001528 1.1 1.2 4.5HOP NM_139211 1.1 1.7 4.5A_24_P739785 A_24_P739785 1.1 1.8 4.5SPAG6 NM_172242 1.0 1.4 4.5INSM1 NM_002196 1.1 1.4 4.5THC2651722 THC2651722 1.1 1.6 4.5THC2706230 THC2706230 1.2 1.7 4.5C19orf31 NM_001014373 0.7 1.7 4.5PPP4R1L NM_018498 1.1 1.1 4.5AK095439 AK095439 1.1 1.6 4.5KCNB2 NM_004770 1.3 1.8 4.5AUTS2 BC011643 1.1 1.1 4.5BC017937 BC017937 1.3 1.6 4.5TCF15 NM_004609 1.1 1.6 4.5PTGIR NM_000960 1.1 1.7 4.4ZSCAN18 NM_023926 0.9 2.7 4.4A_24_P919825 A_24_P919825 1.1 1.1 4.4ANKS6 NM_173551 1.1 1.3 4.4FOXF1 NM_001451 0.9 1.5 4.4AF318318 AF318318 1.1 1.1 4.4MOSC1 NM_022746 1.1 1.1 4.4ACTN2 NM_001103 1.1 1.1 4.4PHLDA1 NM_007350 1.1 1.1 4.4OR2B6 NM_012367 0.6 0.6 4.4ESRRG NM_206594 1.1 1.3 4.4AMIGO1 NM_020703 1.1 1.1 4.4CACNB2 AK128769 1.1 1.6 4.4ENST00000358162 ENST00000358162 0.8 1.1 4.4THC2730567 THC2730567 1.1 1.2 4.4PHACTR1 AB051520 1.1 1.1 4.4NFE2 NM_006163 1.1 1.1 4.4FGFBP1 NM_005130 1.1 1.1 4.4

MOCS1 NM_138928 1.1 2.0 4.4CHRNG NM_005199 1.1 1.1 4.3DTX4 ENST00000227451 1.1 1.8 4.3COL6A1 NM_001848 0.7 1.7 4.3ENST00000389477 ENST00000389477 1.1 1.9 4.3THC2781239 THC2781239 1.1 1.6 4.3LOC650177 XR_018734 1.4 1.5 4.3MAOA NM_000240 0.6 1.5 4.3LOXL4 NM_032211 1.1 1.1 4.3TAC1 NM_003182 1.1 1.1 4.3PARP3 NM_001003935 0.9 2.8 4.3SYT11 NM_152280 1.1 1.5 4.3HSPA12B NM_052970 1.1 1.1 4.3SLC4A4 NM_003759 1.0 2.8 4.3BC017937 BC017937 1.2 1.5 4.3DSP NM_004415 1.1 1.1 4.3TDRD10 NM_182499 1.1 1.2 4.3hCG_2036596 AK124708 1.1 1.1 4.3TNFAIP8L3 NM_207381 0.9 1.5 4.2ZFP14 NM_020917 1.3 1.6 4.2HIST1H2AK BC034487 1.1 1.9 4.2A_32_P191141 A_32_P191141 1.1 1.9 4.2FCER1A NM_002001 1.1 2.0 4.2ENST00000327299 ENST00000327299 1.1 2.0 4.2SYNGAP1 NM_006772 1.2 1.5 4.2AW445156 AW445156 1.1 1.9 4.2CRIP3 NM_206922 1.1 1.1 4.2PHLDA1 NM_007350 1.0 1.2 4.2NPNT NM_001033047 1.1 1.1 4.2LTB4DH NM_012212 1.1 1.1 4.2ADAMTS3 NM_014243 1.1 1.9 4.2THC2668923 THC2668923 0.8 1.4 4.2KAZALD1 ENST00000224809 1.3 2.0 4.2RASD1 NM_016084 0.9 1.4 4.2DKFZP434P211 AL117401 1.5 1.3 4.2C10orf25 NM_001039380 1.1 1.8 4.2AK129542 AK129542 1.7 1.1 4.2A_32_P116088 A_32_P116088 0.7 1.4 4.2

THC2657554 THC2657554 1.1 1.1 4.2A_24_P384604 A_24_P384604 1.1 1.1 4.2GLYAT NM_201648 1.1 1.1 4.1PSG6 NM_002782 1.1 1.3 4.1LRRC49 NM_017691 0.7 1.7 4.1MGC13053 BC006134 1.1 1.8 4.1KRT83 NM_002282 1.1 1.1 4.1A_32_P55438 A_32_P55438 0.7 1.7 4.1ARHGAP28 NM_001010000 1.1 1.6 4.1GFRA1 NM_005264 1.1 1.1 4.1ENST00000254109 ENST00000254109 1.1 1.1 4.1GRAMD1B AY358924 1.1 1.5 4.1FGFR2 NM_022970 1.2 1.7 4.1LOC441601 NR_003034 1.1 1.1 4.1GDF9 NM_005260 1.6 1.1 4.1MOBKL2B NM_024761 1.1 1.6 4.1SPG3A NM_015915 0.9 1.6 4.1KIAA2022 NM_001008537 1.1 1.1 4.1BC017937 BC017937 1.3 1.5 4.1A2M NM_000014 1.1 1.6 4.1C3orf41 AL117530 1.1 1.1 4.1PRRG3 NM_024082 1.1 2.0 4.1FMN2 NM_020066 1.1 1.1 4.0THC2667273 THC2667273 1.7 1.1 4.0AK093987 AK093987 1.1 1.1 4.0C1orf51 NM_144697 1.1 2.1 4.0ENST00000356186 ENST00000356186 1.1 1.8 4.0REG1A NM_002909 1.1 1.5 4.0NEURL NM_004210 0.7 1.1 4.0A_32_P99744 A_32_P99744 1.1 1.9 4.0LOC441258 AK024602 1.2 1.9 4.0LOC54103 AK126364 1.1 1.6 4.0IL18R1 NM_003855 1.1 1.7 4.0THC2591546 THC2591546 1.1 1.6 4.0ANKRD6 NM_014942 1.1 1.1 4.0A_32_P147395 A_32_P147395 1.1 1.1 4.0AW817085 AW817085 1.1 1.6 4.0THC2682319 THC2682319 1.1 1.6 4.0

THC2686110 THC2686110 1.1 2.0 4.0PBLD NM_022129 1.1 1.7 4.0PRKCZ NM_002744 1.2 1.8 4.0PDE4DIP NM_022359 1.1 1.1 4.0MGC16275 BC043607 1.1 1.8 4.0BX102475 BX102475 0.7 1.5 3.9THC2684461 THC2684461 1.1 1.1 3.9EBF3 NM_001005463 1.1 1.1 3.9LOC390705 BC041879 1.1 1.3 3.9THC2670311 THC2670311 1.1 1.4 3.9LOC131873 AL713792 1.1 1.9 3.9DAG1 NM_004393 1.3 1.6 3.9THC2519174 THC2519174 1.1 1.1 3.9AW664702 AW664702 1.1 1.1 3.9LOC400752 ENST00000372127 1.3 1.1 3.9NEFL NM_006158 0.6 0.5 3.9FLJ33790 NM_001039548 1.0 1.7 3.9CTTN NM_005231 0.9 0.9 3.9MMP13 NM_002427 1.1 1.1 3.9PCDHGB4 NM_032098 1.1 1.5 3.9HS3ST3A1 NM_006042 1.1 1.1 3.9AK124399 AK124399 1.1 1.1 3.9THC2646374 THC2646374 1.2 1.1 3.9TPCN2 AL137479 1.4 1.3 3.9THC2500744 THC2500744 1.4 1.4 3.9THC2672319 THC2672319 1.1 1.1 3.9TRIM50 NM_178125 1.1 1.5 3.9DHX34 D50924 1.0 1.5 3.9AL049991 AL049991 1.1 1.6 3.9DMD NM_004023 1.1 1.1 3.8LOC642413 XR_016155 1.1 1.1 3.8ELSPBP1 NM_022142 1.1 1.1 3.8ALDOB NM_000035 0.8 1.5 3.8GATA4 AF318320 1.1 1.6 3.8ANGPT2 ENST00000382726 1.4 1.4 3.8KIAA1841 BC039298 1.1 1.7 3.8FLJ13224 AK023286 1.2 1.1 3.8AK021427 AK021427 1.1 1.1 3.8

GPR109B NM_006018 1.1 1.1 3.8TCF7 NM_003202 1.1 1.3 3.8RAPH1 NM_025252 0.7 1.3 3.8ENST00000318093 ENST00000318093 1.1 1.8 3.8A_24_P874334 A_24_P874334 1.5 1.3 3.8CEACAM19 AK128234 1.0 1.9 3.8KLRF1 NM_016523 1.1 1.1 3.8CTDSPL NM_001008392 1.1 1.1 3.8NO145 NM_001040274 1.1 1.1 3.8THC2558594 THC2558594 1.1 1.2 3.8C22orf31 NM_015370 1.1 1.1 3.8ENST00000332432 ENST00000332432 1.1 1.3 3.8LOC220115 NR_002793 1.1 1.6 3.8CBR4 AK027337 1.3 1.3 3.8BC019241 BC019241 1.1 1.7 3.8FABP3 NM_004102 1.1 1.1 3.8A_23_P145596 A_23_P145596 1.6 1.3 3.8A_24_P928830 A_24_P928830 1.1 1.1 3.8TKTL2 NM_032136 1.1 1.1 3.8FAM110B NM_147189 1.3 1.4 3.8THC2661011 THC2661011 1.1 1.6 3.8FCAMR AY063125 0.6 0.8 3.8A_32_P72682 A_32_P72682 1.1 1.3 3.8DEFB104A NM_080389 1.1 1.1 3.7KIAA1598 NM_018330 1.1 1.1 3.7A_32_P13202 A_32_P13202 1.1 1.3 3.7ABL1 NM_005157 1.4 1.4 3.7A_24_P384119 A_24_P384119 1.1 1.4 3.7LOC339240 NR_001443 1.1 1.3 3.7TMEM132A NM_017870 1.2 1.1 3.7AK128756 AK128756 1.1 1.6 3.7ENST00000390369 ENST00000390369 1.1 1.1 3.7ADAMTS18 NM_139054 1.1 1.1 3.7KCNH5 NM_172376 1.1 1.1 3.7AK055112 AK055112 1.1 1.1 3.7THC2636507 THC2636507 1.1 1.4 3.7DA727827 DA727827 1.1 1.4 3.7PDCD4 NM_145341 0.8 1.8 3.7

NRSN1 NM_080723 1.1 1.1 3.7NR1H4 NM_005123 1.1 1.1 3.7AK021798 AK021798 1.0 1.5 3.7WFDC5 NM_145652 1.1 1.1 3.7THC2540410 THC2540410 1.1 1.5 3.7C3orf64 NM_173654 0.8 0.9 3.7TMEM35 NM_021637 0.7 1.5 3.7ANGPT1 NM_001146 1.1 1.1 3.7CCDC65 NM_033124 1.1 1.5 3.7SYCP2 NM_014258 1.1 1.1 3.7THC2654991 THC2654991 1.1 1.1 3.7GPR126 NM_198569 1.1 1.4 3.7TMPRSS12 NM_182559 1.1 1.1 3.7AK022645 AK022645 1.1 1.1 3.6TITF1 NM_003317 1.1 1.1 3.6AK093927 AK093927 1.1 1.1 3.6C1orf210 NM_182517 1.1 1.1 3.6FOXD1 NM_004472 1.1 1.1 3.6ENST00000358356 ENST00000358356 0.8 1.4 3.6BC030685 BC030685 1.1 1.1 3.6GREM2 NM_022469 1.1 1.5 3.6LMCD1 NM_014583 1.1 1.1 3.6SLFN11 NM_152270 0.8 0.9 3.6AK090480 AK090480 1.1 1.3 3.6AW467174 AW467174 0.9 1.4 3.6AK3L2 NM_001002921 1.1 1.5 3.6A_24_P474384 A_24_P474384 1.1 1.1 3.6RHOV ENST00000220507 0.8 1.7 3.6MOV10L1 NM_018995 1.1 1.1 3.6KRT18P41 XR_016695 0.8 1.7 3.6MGC45438 NM_152459 1.1 1.1 3.6PURG NM_001015508 1.1 1.1 3.6BC031939 BC031939 1.1 1.1 3.6NOPE NM_020962 1.2 1.0 3.6THC2698352 THC2698352 1.1 1.3 3.6ARHGAP6 NM_001174 1.1 1.3 3.6LIPG NM_006033 1.1 1.1 3.6AW978845 AW978845 1.1 1.1 3.6

LILRA5 NM_181879 1.1 1.1 3.5ABCC9 NM_020297 1.1 1.1 3.5ENST00000166133 ENST00000166133 0.7 1.3 3.5ARHGEF4 NM_032995 1.1 1.1 3.5OR4S1 NM_001004725 1.1 1.1 3.5A_23_P395705 A_23_P395705 1.1 1.1 3.5GZMK NM_002104 1.1 1.1 3.5C3orf50 BC011266 1.1 1.3 3.5MERTK U08023 1.1 1.1 3.5AK054684 AK054684 1.1 1.1 3.5CDS1 NM_001263 0.9 1.7 3.5ENST00000317596 ENST00000317596 1.1 1.1 3.5ANGPT2 NM_001147 1.1 1.1 3.5HOXB5 NM_002147 1.1 1.1 3.5THC2656116 THC2656116 1.1 1.1 3.5KCNJ9 ENST00000368088 1.1 1.1 3.5BG719660 BG719660 1.1 1.1 3.5CB154245 CB154245 0.7 0.7 3.5LOC388503 NM_001013640 1.1 1.1 3.5PLA2G3 NM_015715 0.8 1.8 3.5AK026881 AK026881 0.8 1.5 3.5THC2705989 THC2705989 1.1 1.1 3.5MIER2 AB033019 1.1 1.1 3.5AK002066 AK002066 1.2 1.3 3.5TGFBI NM_000358 1.1 1.2 3.5ABCC11 NM_033151 1.1 1.1 3.4HMGCS2 NM_005518 1.1 1.1 3.4THC2516687 THC2516687 1.1 1.1 3.4KIF19 NM_153209 1.1 1.1 3.4BAPX1 NM_001189 1.1 1.2 3.4BG547557 BG547557 1.1 1.1 3.4KLRG2 ENST00000340940 0.8 1.6 3.4BC029927 BC029927 1.1 1.1 3.4BU629094 BU629094 1.3 1.1 3.4TCEAL7 NM_152278 1.1 1.2 3.4RPRM NM_019845 1.1 1.1 3.4SNED1 NM_001080437 1.0 1.0 3.4LOC729356 XR_015521 1.1 1.1 3.4

LOC401052 NM_001008737 1.1 1.1 3.4AK023572 AK023572 1.1 1.1 3.4PRDM9 NM_020227 1.1 1.1 3.4BI758260 BI758260 1.1 1.1 3.3THC2780391 THC2780391 0.9 1.6 3.3PKD1L2 NM_052892 1.1 1.1 3.3SLC40A1 NM_014585 1.1 1.1 3.3ENST00000366822 ENST00000366822 1.1 1.1 3.3ZCCHC2 ENST00000269499 1.1 1.1 3.3BCAR4 CR606007 1.1 1.1 3.3LEMD1 NM_001001552 1.1 1.1 3.3THC2689572 THC2689572 0.7 1.3 3.3A_24_P933410 A_24_P933410 1.1 1.1 3.3BC015129 BC015129 1.1 0.9 3.3GLUL NM_002065 1.1 1.1 3.3LOC388610 NM_001013642 0.7 1.2 3.3THC2657647 THC2657647 1.1 1.1 3.3RAB3C NM_138453 1.1 1.1 3.3ANKRD22 NM_144590 1.1 1.1 3.3BU930695 BU930695 1.1 1.1 3.3PAPSS2 NM_001015880 0.7 0.7 3.3SAA3P AY209188 1.1 1.1 3.3THC2529452 THC2529452 0.6 1.3 3.3DNM3 NM_015569 0.8 1.6 3.3LOC151146 AK021716 1.1 1.1 3.3KCNE1 NM_000219 1.1 1.1 3.3AA729924 AA729924 1.1 1.1 3.3CHRNB4 NM_000750 1.1 1.1 3.2CFTR NM_000492 0.7 1.4 3.2C22orf24 AL050256 1.1 1.1 3.2SRD5A2 NM_000348 1.0 1.2 3.2LOC541473 NM_001013748 1.1 1.1 3.2ENST00000315302 ENST00000315302 0.6 1.1 3.2FLJ13236 NM_024902 1.1 1.0 3.2BC024651 BC024651 1.0 1.2 3.2GPR161 NM_153832 1.0 1.0 3.2PRL NM_000948 0.8 0.7 3.2AF086125 AF086125 0.7 1.4 3.2

THC2533951 THC2533951 0.8 1.3 3.1LOC89944 NM_138342 1.0 0.6 3.1HOXA4 NM_002141 0.7 1.0 3.0A_23_P159163 A_23_P159163 0.8 0.8 3.0A_24_P940385 A_24_P940385 0.7 1.3 3.0MAGED4 NM_030801 0.8 1.3 3.0ARHGAP20 NM_020809 0.7 1.0 2.9A_32_P124392 A_32_P124392 0.9 0.9 2.9AK001062 AK001062 0.7 1.3 2.9CXCL12 NM_199168 0.9 0.9 2.8CR597597 CR597597 0.8 1.0 2.8C1orf115 NM_024709 0.7 0.7 2.8GJA4 NM_002060 0.8 0.7 2.7GCH1 NM_000161 0.6 1.1 2.6DUSP13 NM_001007271 0.9 0.7 2.6CR622072 CR622072 0.6 1.0 2.5COL13A1 NM_005203 0.7 0.6 2.5ROR2 NM_004560 0.8 0.7 2.5