Supplementary Materials and Methods

Antibodies and reagents The goat polyclonal antibodies against TOX3, the rabbit polyclonal antibody against

Ki-67, the mouse monoclonal antibody against BRCA1、DNMT1 and GAPDH, and the

secondary goat anti-rabbit biotinylated (IgG) antibody, rabbit anti-goat HRP-conjugated antibody and goat anti-mouse HRP-conjugated antibody were purchased from Abcam (Cambridge, MA, USA). The rabbit polyclonal antibody against TOX3, the mouse monoclonal antibodies against HA and Myc epitopes were products of Sigma-Aldrich (St. Louis, MO, USA). MTT, DMSO, Albumin from bovine serum (BSA), Mayer’s hematoxylin, 3-3’-diaminobenzidine (DAB), Cisplatin (CDDP), 17-β estradiol (E2), trichostatin A (TSA), G418 and puromycin were also products of Sigma-Aldrich.

cDNA, shRNA and reporter constructs The full length TNRC9 was PCR amplified using forward 5’- GGCCAATCCGGCCATGGATGTGAGGTTCTACC-3’ and reverse 5’- GGCCTCTAAGGCCTCAGAAAATACTGACCTGCGATAATACTTGAGT-3’ primers and subsequently subcloned into SfiI fragment of pCDEF3 vector (Invitrogen, Carlsbad, CA) with an N-terminal HA tag. The HA-TNRC9mut is a TNRC9 DNA binding domain- deleted truncation of HA-TNRC9 with a deletion from 922bp to 1149bp of NM_001080430. The full length CREB was PCR amplified using forward 5’- GGCCAATCCGGCCATGACCATGGAATCTGGAG-3’ and reverse 5’- GGCCTCTAAGGCCTTAATCTGATTTGTGGCAGT-3’ primers and subcloned into SfiI fragment of pCDEF3 vector with an N-terminal Myc tag. The shRNA construct targeting TNRC9 were established using pSuper RNAi system (Oligoengine, Seattle, WA). The targeting regions were 1931bp-1949bp (sh1) and 974bp-992bp (sh2) of NM_001080430. The non-specific control sequence was 5’-GACGTAAACGGCCACAA GT-3’. A 602 subregion of BRCA1 promoter (-458 to +145) was PCR amplified from human genomic DNA using forward 5’-CTCGAGACCTTTCATTCCGCAACGCATG- 3’ and reverse 5’- AAGCTTTCCCGGGACTCTACTACCTTTAC-3’ primers (1) and subsequently subcloned into XhoI-BglII fragment of pGL4 basic vector (Promega,

1 Madison, WI). It was named as pGL4-promBRCA1.

Quantitative real-time PCR All the quantitative real-time PCR were performed on 7500 Real-Time PCR system (Applied Biosystems, Carlsbad, CA) using GoTaq® qPCR Master Mix (Promega, Madison, WI). The genomics region of FUT2 and PTPN4 were used as references to assess the copy number variation of TNRC9 genomic region. Primer sequences were as follows: TNRC9 exon3 forward 5’-CTTGGGGACGAGGAATTCGA-3’, reverse 5’- GTAATGGAAGGGAGGTCCA-3’; TNRC9 exon4 forward 5’-ATCGTCCACATGACC GATG-3’, reverse 5’-CTCTTCATTGATGGAGCTG-3’; FUT2 forward 5’- ATCTTCGTGGTCACCAGTAATGG-3’, reverse 5’-GGTTACACTGTGTGAGTAGAG C-3’; PTPN4 forward 5’-ACGCACGGTCCCATAGTATC-3’, reverse 5’- AAATAGTG

GTGCCTCCTTGG-3’. When min (CtFUT2, CtPTPN4) - max (CtTNRC9exon3, CtTNRC9exon4) >1, the sample was considered to have a copy number amplification of TNRC9 genomic DNA. HPRT1 was used as the internal reference to assess the mRNA expression level of TNRC9. The reverse transcription of total RNA was performed by GoTaq® 2-Step RT- qPCR System (Promega, Madison, WI). The primer sequences used to amplify TNRC9 cDNA were 5’-TGCCTCACACATCTCCTTCAC-3’ and 5’- TTGGAGTCTTGGGCTTCTTGC-3’, and HPRT1 cDNA were 5’- TGACACTGGCAAAACAATGCA-3’ and 5’-GGTCCTTTTCACCAGCAAGCT-3’. The bisulfite-converted DNA was analyzed by quantitative PCR using primers for methylated BRCA1 promoter region: forward 5’-TCGTGGTAACGGAAAAGCGC-3’ (-38 to -19) and reverse 5’-AACGAACTCACGCCGCGCAA-3’ (+11 to +30) and unmethylated BRCA1 promoter region: forward 5’-TTGAGAGGTTGTTGTTTAGTGG- 3’ (-74 to -43) and reverse 5’-AACAAACTCACACCACACAA-3’ (+11 to +30) (2). The 3’ end of DHFR was used as a reference: forward 5’- TTGATGTTTAGGAGGAGAAAGG-3’ and reverse 5’- AACCCAACAATATCAAAAACTA-3’. The copies of methylated or unmethylated BRCA1 promoter were calculated using 2-(CtBRCA1-CtDHFR). The combination of methylated BRCA1 promoter and unmethylated BRCA1 promoter was used as the total copies of BRCA1 promoter. The percentage of methylated BRCA1 promoter was

2 calculated by dividing the total copies of BRCA1 promoter.

Bisulfite sequencing of BRCA1 promoter

To amplify a region of BRCA1 promoter, the bisulfite-converted DNA from TNRC9 abrogated ZR-75-1 cells and from control cells were amplified using a nested PCR (3). The first run was accomplished by the forward primer 5’- GGGGTTGGATGGGAATTGTAG-3’(-686 to -666 of BRCA1 gene) and reverse primer 5’-CTCTACTACCTTTACCCAAAACA-3’ (+130 to +108). One tenth of the first run amplification was re-amplified with forward primer 5’- GTTTATAATTGTTGATAAGTATAAG-3’(-592 to -568) and reverse primer 5’- AAAACCCCACAACCTATCCC-3’(+66 to +47). The second run PCR product was purified and cloned into a T vector-pGEMT (Promega). Twenty clones of each sample were randomly selected and sequenced.

Immunohistochemistry Formalin fixed and paraffin embedded sections were cut at 5 micron thick and were deparaffinized and rehydrated through 3 concentrations of alcohol. Endogenous

peroxidase activity was blocked with 3% H2O2 for 15 minutes. Antigen retrieval was carried out in 0.01 M citrate buffer, pH 6.0, at 95°C for 20 minutes, followed by 20 minutes cooling at room temperature. Nonspecific binding was blocked using PBST containing 5% BSA for 1 hr. Sections were incubated overnight with goat anti-TNRC9 (1:50) and mouse anti-BRCA1 antibodies (1:50) at 4 °C, followed by HRP-conjugated secondary antibodies (1:500) for 1 hour at room temperature. Antibody binding was revealed with DAB (DAKO, Denmark) as chromogen. In between steps sections were washed with PBST for 3 times, each for 7 min. Sections were counterstained with Mayer’s hematoxylin, dehydrated and mounted. Images were obtained using a bright field microscope (AxioVision software). High-grade and low-grade breast cancer samples were included in this study. Sections incubated with non-immune control sera acted as negative control.

Immunoprecipitation and immunoblotting Cells were lysed with RIPA buffer (50mM Tris pH7.4, 100mM Nacl, 0.25% Na- deoxycholate, 1% NP40, 0.1% SDS) containing 1X protease inhibitors cocktail (Sigma- Aldrich, St. Louis, MO). Equal amounts of cell lysates were separated on SDS-PAGE

3 gel, transferred to PVDF membrane and probed with primary antibodies. Bands were visualized using Geliance 600 Imaging System (PerkinElmer, Waltham, MA), in conjugation with HRP-conjugated secondary antibodies and ImmobilonTM western chemiluminescent HRP substrate (Millipore, Billerica, MA). For the detection of interaction between TNRC9 and CREB, 107 transfected HEK293 cells were lysed in RIPA buffer. Lysates were precleared with Protein A/G Plus Agarose beads (Santa Cruz Biotechnology, Santa Cruz, CA) and 2 mg IgG for 2 h at 4 °C. The precleared lysates were immunoprecipitated with anti-TNRC9 or anti-HA for over 4 h at 4 °C. The immunoprecipitated samples were washed three times with lysis buffer, resolved by SDS–PAGE and then subjected to immunoblotting analysis with anti-Myc.

Mouse model Cells for injection are agitated slowly on a Vortex mixer in a 50 ml Falcon tube to ensure even suspension. Enough cells are then withdrawn to inoculate 5 mice; that is, ~0.5 ml of a 3x107 cell/mL suspension. The syringe is then gently inverted (containing the glass bead) to ensure even suspension. A 27 Gauge, ½ inch Precision Glide needle (BD, Franklin Lakes, NJ) is then inserted onto the syringe and primed. NU/NU nude mice (Charles River Laboratories, Wilmington, MA) are anesthetized by placing them in a 5% Isoflurane chamber. Once the mice are deeply under anesthesia, mice are removed individually, placed into the biological-safety cabinet and prepared for injection (positioned prone and upper right flank wiped with a 70% ethanol pad). The syringe is again gently inverted 3 times to ensure even cell suspension. Without tenting the skin, 0.1 ml of the cell suspension (containing approximately 3 million cells) is injected into the upper right flank of the mouse, subcutaneously. Each mouse is then placed into a separate chamber until conscious before being returned to its original cage. Tumors were monitored at 2-3 day intervals for a total of 28 days. Tumor size (width and length) was recorded, the skin overlaying the tumor was inspected and the mice weighed. After 28 days, tumors were surgically excised, measured with digital calipers and placed into 10% neutral buffered formalin. Tumors were then embedded in paraffin, sectioned and stained with hematoxylin and eosin (H&E) or immunostained for Ki-67 (proliferative cells) a proliferative cell marker, using a polyclonal IgG primary antibody (rabbit; abcam) and

4 anti-rabbit biotinylated (IgG) secondary antibody (goat; Abcam) with Vectastain Elite ABC Kit (Vector Laboratories, Burlingame, CA) and methyl green counterstain (Vector Laboratories, Burlingame, CA). All mouse experiments were reviewed and approved by the Institutional Animal Care and Use Committee at Brown University.

In silico assays for the expression of TNRC9 and BRCA1 In silico assays were performed on 266 early breast cancer patients. Transcriptional data were retrieved from NCBI GEO database (GSE21653) and further analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html), Partek Genomics Suite (PARTEK, St Louis, MO), Stanford Cluster Program and TreeView software (4). Genes were projected using log2 intensity and gene ratios were average corrected across experimental samples and displayed according to uncentered correlation algorithm. Similar to breast cancer analysis, in silico assays were performed on a cohort of 200 ovarian cancer patients, kindly provided by Dr. George Coukos (University of Pennsylvania, PA, USA) and further processed by Department of Transfusion Medicine, National Institute of Health, Bethesda, MD, USA using Affymetrix U133.

Supplementary references

1. DiNardo DN, Butcher DT, Robinson DP, Archer TK, Rodenhiser DI. Functional analysis of CpG methylation in the BRCA1 promoter region. Oncogene 2001;20:5331-40.

2. Wei M, Grushko TA, Dignam J, Hagos F, Nanda R, Sveen L, et al. BRCA1 promoter methylation in sporadic breast cancer is associated with reduced BRCA1 copy number and chromosome 17 aneusomy. Cancer Res 2005;65:10692-99.

3. Rice JC, Massey-Brown KS, Futscher BW. Aberrant methylation of the BRCA1 CpG island promoter is associated with decreased BRCA1 mRNA in sporadic breast cancer cells. Oncogene 1998;17:1807-12.

4. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95:14863-68.

5 Supplementary Figures

A C

B

Supplementary Figure 1. TNRC9 promoted cell proliferation in MDA-MB-231 breast cancer cells. A, HA-tagged TNRC9 expression in MDA-MB-231 cells. MDA-MB-231 was transfected with pCDEF3-HA-TNRC9 or empty vector and the stable transfected cells were obtained with the screening using 3mg/ml G418. B, Ectopic-expression of TNRC9 promoted the growth of MDA-MB-231 cells. MDA-MB-231 cells were transfected with HA-TNRC9 and screened with 3 mg/ml G418. The proliferation of cells ectopic-expressing TNRC9 was measured by MTT assay. *P=0.01. C, Ectopic expression of TNRC9 accelerated the wound healing of MDA-MB-231 cells. Wound closures were photographed at indicated time. Experiments were done three times and each experiment showed similar result. The scale bar represents 200µm.

Supplementary Figure 2. shRNA-mediated knockdown of TNRC9. Stable cells with shRNA against TNRC9 were obtained with the screening using 0.5µg/ml puromycin. The knockdown effect was examined by immunoblotting with anti-TNRC9 antibodies.

6

Supplementary Figure 3. H&E staining of tumors (10×Magnification) from xenograft nude mice subcutaneously injected with control ZR-75-1cells (upper row I – V) were compared with those injected with TNRC9-depeltion ZR-75-1 cells (lower row VI – VIII, no palpable tumor in two mice). ‘-’ represents 400μm.

Supplementary Figure 4. Knocking-down TNRC9 sensitizes cancer cells to apoptosis signal. A, Cells were exposed to 200 µW/cm2 UV for indicated time and then incubated for 24 hours. The quantity of viable cells was determined by MTT assay. *P=0.030, ★P=0.017. B, Cells were exposed to normal or serum-free medium for indicated times. The proportion of cells exposure to serum-free medium/cells exposure to normal medium was quantified by MTT assay. *P=0.005, ★P=0.006. C, Cells were exposed to cisplatin of indicated concentration for 24 hours and then the quantity of viable cells was determined by MTT assay. *P=0.009, ★P=0.003.

7 Supplementary Figure 5. BRCA1 and TNRC9 expression in TNRC9 abrogated and control cells.

Supplementary Figure 6. The expression profile of TNRC9 knockdown MCF-7 cells. A, The differential expression profile between TNRC9 knockdown and control MCF-7 breast cancer cells. TNRC9-knockdown cells (triplicate): S1, S2&S3. MCF-7 control cells (triplicate): C1, C2&C3. B, Cluster diagram of Affymetrix microarray data using PARTEK to showing 227 genes differentially expressed between TNRC9 knockdown and control cells. C, The expression level of BRCA1 in TNRC9 knockdown and control cells.

8

Supplementary Figure 7. In silico analysis of TNRC9 and BRCA1 gene expression among ovarian cancer patients. Self-organizing heat map displaying the expression of TNRC9 and BRCA1 genes, segregated the 200 patients with ovarian cancer into four groups characterized by high expression of both TNRC9 and BRCA1 (Fig. S7-I, group a), high expression of TNRC9 and low expression of BRCA1 (Fig. S7-I, group b), low expression of both TNRC9 and BRCA1 (Fig. S7-I, group c) and low expression of TNRC9 and high expression of BRCA1 (Fig. S7-I, group d). The obtained results showed that 105 ovarian cancer patients, were characterized by inverse expression of TNRC9 and BRCA1 genes. The negative correlation between the expression of TNRC9 and BRCA1, was highlighted by performing a heat map considering the expression values of the two genes only in the 105 selected patients (Fig. S7-II) and by assaying for the same cohort of patients, a similarity matrix based on Pearson correlation (Fig. S7-III).

9

Supplementary Figure 8. The effects of TNRC9 on luciferase activity driven by BRCA1 promoter. MCF7 cells were transfected with control luciferase plasmid pGL4, BRCA1 promoter driven pGL4 plasmid pGL4-promBRCA1, TNRC9 expression plasmid HA-TNRC9 and pGL4-promBRCA1, and TNRC9 mutant expression plasmid HA- TNRC9mut and pGL4-promBRCA1, respectively. Twenty-four hours after transfection, cells were processed for reporter assay. *P=0.022, **P=0.001, ***P>0.05.

Supplementary Figure 9. Bisulfite sequencing of the BRCA1 promoter. The percentage represents the proportion of clones with methylated CpG at this specific position of BRCA1 promoter relative to the 20 random analyzed clones.

10 Supplementary Table 1 The list of transcripts significantly altered in TNRC9 knockdown MCF-7 cells comparing to control MCF-7 cells

Column ID Gene Symbol p-value Fold-Change* 201030_x_at LDHB 0.000116812 -2.94615 231505_s_at SFXN4 0.000277663 -1.50934 235614_at TMEM151A 0.000531331 -1.51874 209687_at CXCL12 0.000802531 -3.15138 206278_at PTAFR 0.00110997 -1.63433 214362_at RGS12 0.0013439 -1.51609 222470_s_at UQCC 0.00180586 -1.52812 214316_x_at --- 0.00213315 -1.70215 213564_x_at LDHB 0.00232679 -4.06623 211671_s_at NR3C1 0.00241422 -1.53499 209266_s_at SLC39A8 0.00262686 -1.70593 210609_s_at TP53I3 0.00264731 -1.52218 203666_at CXCL12 0.00291463 -2.2122 219189_at FBXL6 0.0039313 -1.54296 221973_at --- 0.00435717 -1.71033 243285_at LOC283335 0.00472133 -1.5446 241477_at NEIL1 0.00539677 -1.50491 231983_at C1orf69 0.00579034 -1.54414 201565_s_at ID2 0.00587015 -2.6642 216163_at --- 0.0067285 -1.55826 1567013_at NFE2L2 0.00701897 -2.37274 211920_at CFB 0.00735562 -1.63717 219424_at EBI3 0.0075202 -1.51431 226748_at LYSMD2 0.00801316 -1.54468 225428_s_at DDX54 0.00873112 -1.58583 205806_at ROM1 0.00883323 -1.50446 239663_x_at LARP1 0.00894443 -1.50958 216289_at GPR144 0.0106454 -1.63068 226063_at VAV2 0.0116539 -1.53944 244193_at DNAJC22 0.011682 -1.81044 219158_s_at NAA15 0.0117037 -1.6423 213740_s_at LOC399904 0.0123489 -1.60638 213931_at ID2 /// ID2B 0.0136188 -1.88144 222436_s_at VPS24 0.0138271 -1.5529 226192_at AR 0.0150705 -1.75403 214630_at CYP11B2 0.0162535 -1.53382 211657_at CEACAM6 0.0167308 -3.08395 212113_at ATXN7L3B 0.0170896 -1.70289 215427_s_at ZCCHC14 0.0171304 -1.53555 238267_s_at --- 0.0173058 -1.57718 201566_x_at ID2 0.0175561 -1.85033 243297_at --- 0.0177299 -1.57061 211000_s_at IL6ST 0.01783 -1.65292 235092_at --- 0.017872 -1.60757 1552627_a_at ARHGAP5 0.0182808 -1.51731 203196_at ABCC4 0.0185591 -1.75746

11 208003_s_at NFAT5 0.0187131 -1.6257 236249_at IKBIP 0.0197623 -1.62611 211621_at AR 0.0199617 -1.53484 244882_at TNRC18 0.02155 -1.54518 237159_x_at AP1S3 0.0217821 -1.54699 1567377_at DNAH1 0.0220993 -1.50052 239507_at LOC151300 0.0221079 -1.50805 242138_at DLX1 0.0223133 -2.14271 203833_s_at TGOLN2 0.023237 -1.50018 219165_at PDLIM2 0.0241086 -1.58629 204909_at DDX6 0.0242473 -1.516 234536_at SARDH 0.0244331 -1.63297 242317_at HIGD1A 0.0245749 -1.92317 204863_s_at IL6ST 0.025423 -1.64374 223168_at RHOU 0.0254461 -1.89395 203757_s_at CEACAM6 0.0262893 -3.10961 210762_s_at DLC1 0.0264771 -2.60915 211653_x_at AKR1C2 0.0269622 -1.90985 209485_s_at OSBPL1A 0.0271521 -1.51992 237327_at APH1A 0.0276974 -1.50386 241670_x_at LOC729177 0.0280749 -1.55482 222857_s_at KCNMB4 0.0281108 -1.60837 218006_s_at ZNF22 0.028236 -1.75131 1555450_a_at NAA16 0.0290237 -1.57284 217937_s_at HDAC7 0.029078 -1.56721 225325_at MFSD6 0.0293903 -1.7615 212010_s_at CDV3 0.0295248 -1.60589 217322_x_at --- 0.0303504 -1.59571 217744_s_at PERP 0.032935 -1.58087 241211_at --- 0.0330642 -1.53957 231268_at LOC645895 /// MYBL1 0.0330716 -1.53486 219528_s_at BCL11B 0.033279 -1.57683 219998_at HSPC159 0.033461 -1.66773 223551_at PKIB 0.0341856 -2.07982 238514_at TMEM25 0.0353072 -1.57966 222197_s_at --- 0.0369808 -1.50747 241671_x_at FLJ22536 0.0376248 -1.65916 208158_s_at OSBPL1A 0.0381004 -1.5682 225721_at SYNPO2 0.0395082 -1.5003 228969_at AGR2 0.0408085 -1.63933 244348_at --- 0.0409354 -1.5089 217437_s_at TACC1 0.0410605 -1.54769 1554690_a_at TACC1 0.0413307 -1.72351 222699_s_at PLEKHF2 0.0416873 -1.52406 232682_at MREG 0.0418256 -1.62002 209692_at EYA2 0.0426259 -1.63937 1554667_s_at METTL8 0.0428259 -1.60787 224848_at CDK6 0.0430282 -1.61812 205565_s_at FXN 0.0438143 -1.72028 221896_s_at HIGD1A 0.0465297 -1.66518

12 236356_at NDUFS1 0.0473154 -1.70916 212007_at UBXN4 0.048175 -1.65941 217845_x_at HIGD1A 0.0481774 -1.58356 202439_s_at IDS 0.0483393 -1.50011 204330_s_at MRPS12 0.0487142 -1.50303 228996_at RC3H1 0.0488329 -1.61747 236429_at ZNF83 0.0490926 -1.95147 239207_at KDM5C 4.72E-05 1.52132 219236_at PAQR6 0.000331724 1.53737 226034_at --- 0.00103306 1.51991 215314_at --- 0.0010368 1.73701 239726_at --- 0.00117999 2.3411 225804_at CYB5D2 0.00119938 1.55631 225012_at HDLBP 0.00120905 1.51632 216338_s_at YIPF3 0.00125938 1.57649 236180_at --- 0.00132404 1.5685 218918_at MAN1C1 0.00158643 1.63443 202479_s_at TRIB2 0.00167985 1.6103 203439_s_at STC2 0.00168879 1.60554 216903_s_at CBARA1 0.0017552 1.50283 203071_at SEMA3B 0.00195065 2.05147 213110_s_at COL4A5 0.00212872 2.23305 1557538_at --- 0.00215412 1.65256 201631_s_at IER3 0.00216271 2.89811 208919_s_at NADK 0.00234221 1.52936 225177_at RAB11FIP1 0.00250245 1.575 217523_at CD44 0.00264196 1.99127 218821_at NPEPL1 0.00268065 1.68646 243963_at SDCCAG8 0.00276975 1.68559 219154_at TMEM120B 0.00318038 1.79519 1553789_a_at C21orf58 0.00319241 1.61763 226869_at MEGF6 0.00335711 1.99005 244358_at --- 0.00354392 1.67941 207695_s_at IGSF1 0.00354563 2.13418 213035_at ANKRD28 0.00391346 1.61541 212344_at SULF1 0.00479318 1.95965 240218_at DSCAM 0.00506321 1.61235 233674_at --- 0.00514672 1.55885 225262_at FOSL2 0.0052223 1.56875 230818_at --- 0.00525851 1.77398 225342_at AK3L1 0.00555599 1.67995 202478_at TRIB2 0.00563403 4.42951 213745_at ATRNL1 0.00565052 2.11027 37590_g_at --- 0.00576888 1.59569 227088_at PDE5A 0.00581729 1.60024 36545_s_at SFI1 0.00584449 2.01342 232307_at --- 0.00607528 2.04012 212741_at MAOA 0.0062572 1.70766 1552790_a_at SEC62 0.00632087 1.54092 220414_at CALML5 0.00649882 2.45404

13 210871_x_at SSX2IP 0.00650241 1.62845 224476_s_at MESP1 0.00679922 1.96601 241685_x_at --- 0.00683267 1.56256 224783_at FAM100B 0.00694938 1.61927 242075_at --- 0.00742598 1.57335 214194_at DIS3 0.00767871 1.53016 209005_at FBXL5 0.00773017 1.51828 213069_at HEG1 0.007866 1.56568 1557553_at PPP1R12B 0.00828926 1.5695 222222_s_at HOMER3 0.0085404 1.58609 212014_x_at CD44 0.0088509 1.86916 228476_at KIAA1407 0.00886163 1.57864 40569_at MZF1 0.00896241 1.50023 229876_at PHKA1 0.00897396 1.53165 226956_at MTMR3 0.00900933 1.50988 214197_s_at SETDB1 0.00931179 1.51018 240192_at FLJ45983 0.00945755 1.57977 213139_at SNAI2 0.00950848 1.54402 212135_s_at ATP2B4 0.00970201 2.24601 224728_at ATPAF1 0.00975001 1.74747 219279_at DOCK10 0.0100385 1.70885 212942_s_at KIAA1199 0.0101481 1.59889 1569477_at --- 0.0103033 1.68511 202234_s_at SLC16A1 0.0104444 1.55062 229253_at THEM4 0.0108573 1.64196 220917_s_at WDR19 0.0112839 1.63326 219045_at RHOF 0.0115579 1.57394 225949_at NRBP2 0.0117677 1.508 213686_at --- 0.0118178 1.8215 234222_at --- 0.0120985 2.00412 203568_s_at TRIM38 0.0121446 1.59435 236427_at --- 0.0123701 1.73111 228384_s_at PYROXD2 0.012416 1.60843 203939_at NT5E 0.0127762 4.8097 237591_at NCRNA00173 0.0129861 1.79713 213215_at AP3S2 0.0131437 1.59059 228182_at ADCY5 0.0131449 1.83755 210064_s_at UPK1B 0.0132415 1.57405 215203_at GOLGA4 0.0138358 1.51257 220196_at MUC16 0.014167 2.09215 204489_s_at CD44 0.0145381 1.60215 226275_at MXD1 0.015187 2.42219 212963_at TM2D1 0.0151907 1.51876 202187_s_at PPP2R5A 0.0152215 1.88036 229699_at LOC100129550 0.015284 1.95561 239923_at --- 0.0156012 1.56796 209733_at MID2 0.016073 1.5243 1552623_at HSH2D 0.0160946 2.02379 236439_at --- 0.016187 1.5213 209442_x_at ANK3 0.0162166 1.52195

14 1553994_at NT5E 0.0162173 2.26065 200766_at CTSD 0.0164692 1.65981 213172_at TTC9 0.0165154 1.72591 234359_at --- 0.016689 1.75874 205726_at DIAPH2 0.0168843 1.58227 213657_s_at --- 0.0170958 1.50573 237460_x_at C14orf182 0.017147 1.52874 233632_s_at XRN1 0.0175998 1.59652 238883_at --- 0.0176377 1.72712 211851_x_at BRCA1 0.0178917 1.5478 207826_s_at ID3 0.0188828 1.59329 218862_at ASB13 0.0191598 1.62195 230563_at RASGEF1A 0.0194545 1.73258 1555779_a_at CD79A 0.0195468 1.52243 222108_at AMIGO2 0.0195563 2.33874 223401_at C17orf48 0.0202967 1.55165 203438_at STC2 0.0204857 1.83631 200632_s_at NDRG1 0.0214965 1.97786 216675_at --- 0.0217989 1.64549 204595_s_at STC1 0.0223853 2.32449 230746_s_at LOC100288985 0.0227408 2.60579 222854_s_at GEMIN8 0.0228627 1.72726 219961_s_at PLK1S1 0.0233274 1.60454 209835_x_at CD44 0.0257667 1.82599 227929_at --- 0.0258777 1.99942 207950_s_at ANK3 0.0264852 1.9687 223946_at MED23 0.0264953 1.52993 1563057_at --- 0.0270798 1.99506 218822_s_at NPEPL1 0.0271864 1.50717 204597_x_at STC1 0.027392 2.06814 210410_s_at C6orf26 /// MSH5 0.027732 1.71621 203059_s_at PAPSS2 0.0283142 1.70862 230031_at HSPA5 0.0284947 1.50672 219863_at HERC5 0.0287566 1.61788 233700_at --- 0.0288282 1.54465 203585_at ZNF185 0.0290022 1.62714 230669_at RASA2 0.0291669 1.64532 230630_at AK3L1 0.030271 1.55389 228208_x_at ZNF354C 0.0305871 1.54551 213744_at ATRNL1 0.0306936 1.87035 1552714_at CREG2 0.0307032 2.41287 237563_s_at --- 0.0308625 1.52562 230518_at MPZL2 0.0312179 1.67329 218064_s_at AKAP8L 0.0313488 1.52146 212209_at MED13L 0.0323091 1.54649 209605_at TST 0.0334759 1.65304 232944_at --- 0.0350382 1.82317 241363_at EXD3 0.0355537 1.86934 228298_at FAM113B 0.03629 2.04571 220486_x_at TMEM164 0.03648 1.63956

15 237262_at --- 0.0369361 1.63842 244579_at --- 0.0373358 1.65996 204733_at KLK6 0.0378427 2.70206 1555950_a_at CD55 0.0383022 1.59749 212063_at CD44 0.0389995 1.70058 1553910_at NBPF4 0.0391413 1.73596 224938_at NUFIP2 0.0397107 1.58078 204924_at TLR2 0.0403482 1.50711 219995_s_at ZNF750 0.0403931 1.74991 212315_s_at NUP210 0.040516 1.59036 214657_s_at NEAT1 0.040838 1.52757 232881_at GNASAS 0.0411765 1.53055 204872_at TLE4 0.0412417 2.10418 241837_at --- 0.0413966 1.51615 217257_at SH3BP2 0.0414129 1.50668 232855_at --- 0.0437694 1.66263 238047_at ARHGAP36 0.044855 2.59537 205278_at GAD1 0.0459888 1.82284 202949_s_at FHL2 0.0463728 2.0575 223179_at YPEL3 0.0464826 1.54967 201124_at ITGB5 0.0465318 1.5324 227620_at SLC44A1 0.046559 1.58737 204490_s_at CD44 0.0467825 1.8906 239851_at --- 0.0475366 1.51149 228188_at FOSL2 0.0480024 2.14449 209193_at PIM1 0.0481588 1.58308 227041_at SESTD1 0.0481709 1.64819 215867_x_at CA12 0.0487135 1.51428 235273_at DYX1C1 0.048917 1.55939 219717_at DCAF16 0.0495626 1.61139 217810_x_at LARS 0.0499357 1.52838

* P<0.05

16