2: additional support for lres using oncomine data sets. · additional file 2: additional support...

Additional File 2: Additional support for LRES using Oncomine data sets. Each LRES region was further interrogated at the probe set level in additional clinical expression data sets. Results of Exp1 and Exp2 are displayed against nine large Oncomine studies, where local prostate cancer samples were compared with normal prostate samples (see Fig. 1). The name of each study and the number of samples are shown as track names. In addition, results from 5-Aza-dC treatment of prostate cancer cell lines are given in separate tracks. In the 'LRES' track, LRES regions are indicated by black bars. Colours legends are shown at the bottom of each graph.

© 2010 Macmillan Publishers Limited. All rights reserved.

chr1:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N

Dhanasekaran:59T/22N

Yu:64T/23N

Tomlins:30T/22N

Dhanasekaran_2:25T/12N

Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

24500000 25000000 25500000

1p36.11

FUCA1

CNR2

PNRC2

FUSIP1

FUSIP1

MYOM3

IL22RA1

IL28RA

IL28RA

RefSeq genes:

IL28RA

GRHL3

GRHL3

GRHL3

C1orf201

NPAL3

RCAN3

C1orf130

SRRM1

CLIC4

RUNX3

RUNX3

SYF2

SYF2

C1orf63

RHD

RHD

TMEM50A

RHCE

RHCE

RHCE

RHCE

TMEM57

LDLRAP1

MAN1C1

LRES region 01: chr1:24,352,234-25,562,439

On

co

min

e

Oncomine studies: probe set with decreased expression (Q-value < 0.05)

probe set not changed or below detection

probe set with (Q-value < 0.05)increased expression

exp1 / exp2:

Color legends: microarray data - local prostate cancer vs. normal prostate

Color legend: microarray data - prostate cancer cell lines after 5-Aza-dC treatment

probe set with decreased expression (log2[FC] < -1.5 and p < 0.05)

probe set below detection (hybridization signal below 20 across all samples)

probe set not changed

probe set with increased expression (log2[FC] > 1.5 and p < 0.05)

all other probe sets

probe set with increased expression (log2[FC] > 2.0)


chr1:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

65000000 66000000 67000000 68000000 69000000

1p31.3

1p31.2

FOXD3

ALG6

ITGB3BP

EFCAB7

DLEU2L

PGM1

ROR1

ROR1

UBE2U

CACHD1

RAVER2

JAK1

AK3L1

AK3L1

AK3L1

DNAJC6

LEPR

LEPR

LEPR

LEPROT

PDE4B

PDE4B

PDE4B

PDE4B

SGIP1

TCTEX1D1

INSL5

WDR78

WDR78

MIER1

MIER1

MIER1

MIER1

MIER1

MIER1

SLC35D1

C1orf141

IL23R

IL12RB2

SERBP1

SERBP1

SERBP1

SERBP1

GADD45A

GNG12

DIRAS3

GPR177

GPR177

RPE65

DEPDC1

DEPDC1

LRES region 02: chr1:63,827,908-67,304,849and

LRES region 03: chr1:67,922,332-68,689,230

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr1:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

97500000 98000000 98500000 99000000 99500000 100000000 100500000

1p21.3

1p21.2

PTBP2

DPYD

SNX7

SNX7

PAP2D

PAP2D

LPPR4

PALMD

FRRS1

AGL

AGL

AGL

AGL

AGL

AGL

SLC35A3

HIAT1

SASS6

CCDC76

LRRC39

DBT

RTCD1

RTCD1

LRES region 04: chr1:97,314,887-99,933,823

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr1:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

109900000 109950000 110000000 110050000 110100000

1p13.3

ATXN7L2

CYB561D1

CYB561D1

CYB561D1

CYB561D1

CYB561D1

AMIGO1

GPR61

GNAI3

GNAT2

AMPD2

AMPD2

AMPD2

GSTM4

GSTM4

GSTM4

GSTM2

GSTM2

GSTM1

GSTM1

GSTM5

GSTM3

GSTM3

EPS8L3

EPS8L3

EPS8L3

LRES region 05: chr1:109,883,032-110,086,183

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr1:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

117000000 117500000 118000000

1p13.1

1p12

CD58

IGSF3

IGSF3

CD2

PTGFRN

IGSF2

TTF2

TRIM45

VTCN1

MAN1A2

FAM46C

GDAP2

GDAP2

WDR3

SPAG17

LRES region 06: chr1:117,253,202-117,973,534

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr1:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

206000000 207000000 208000000

1q32.1

1q32.2

SRGAP2

SRGAP2

IKBKE

RASSF5

RASSF5

RASSF5

LGTN

DYRK3

DYRK3

MAPKAPK2

MAPKAPK2

IL10

IL19

IL19

IL20

IL24

IL24

FAIM3

PIGR

FCAMR

FCAMR

FCAMR

C1orf116

C1orf116

YOD1

PFKFB2

PFKFB2

C4BPB

C4BPB

C4BPB

C4BPB

C4BPB

C4BPA

CD55

CD55

CR2

CR2

CR1

CR1

CR1L

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD46

CD34

CD34

PLXNA2

LOC642587

CAMK1G

LAMB3

LAMB3

LAMB3

G0S2

HSD11B1

HSD11B1

TRAF3IP3

C1orf74

IRF6

C1orf107

SYT14

C1orf133

SERTAD4

HHAT

HHAT

LRES region 07: chr1:205,327,810-208,023,288

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr2:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

121000000 121500000 122000000

2q14.2

2q14.3

PTPN4

EPB41L5

TMEM185B

RALB

INHBB

GLI2

TFCP2L1

CLASP1

CLASP1

CLASP1

RNU4ATAC

MKI67IP

TSN

LRES region 08: chr2:120,725,884-122,124,522

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr2:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

178000000 178500000 179000000 179500000 180000000

2q31.1

2q31.2

HNRNPA3

NFE2L2

AGPS

TTC30B

TTC30A

PDE11A

PDE11A

PDE11A

PDE11A

RBM45

OSBPL6

OSBPL6

PRKRA

PRKRA

PRKRA

DFNB59

FKBP7

FKBP7

PLEKHA3

TTN

TTN

TTN

TTN

TTN

CCDC141

SESTD1

ZNF385B

ZNF385B

ZNF385B

LRES region 09: chr2:177,784,668-179,838,744

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr3:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

30000000 31000000 32000000 33000000

3p24.1

3p23

3p22.3

ZCWPW2 RBMS3

RBMS3

RBMS3

TGFBR2

TGFBR2

GADL1

STT3B

OSBPL10

ZNF860

GPD1L

CMTM8

CMTM7

CMTM7

CMTM6

DYNC1LI1

CNOT10

TRIM71

CCR4

GLB1

GLB1

GLB1

FLJ45032

FLJ45032

CRTAP

LRES region 10: chr3:29,296,947-32,387,817

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr3:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

58000000 58500000

3p14.3

3p14.2

PDE12

ARF4

FAM116A

SLMAP

FLNB

DNASE1L3

ABHD6

RPP14

RPP14

PXK

PDHB

KCTD6

KCTD6

ACOX2

FAM107A

FAM107A

FAM3D

LRES region 11: chr3:57,717,068-58,550,685

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr3:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

189000000 189500000 190000000 190500000 191000000 191500000 192000000

3q27.3

3q28

ST6GAL1

ST6GAL1

ST6GAL1

RPL39L

RTP1

MASP1

MASP1

MASP1

RTP4

SST

RTP2

BCL6

BCL6

BCL6

FLJ42393

LPP

TPRG1 TP63

TP63

TP63

TP63

TP63

TP63

LEPREL1

LEPREL1

CLDN1

CLDN16

TMEM207

IL1RAP

IL1RAP

SNAR-I

LRES region 12: chr3:188,920,859-191,523,911

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr4:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

154500000 155000000

4q31.3

TIGD4

ARFIP1

ARFIP1

ARFIP1

FHDC1 TRIM2

TRIM2

ANXA2P1

MND1

KIAA0922

KIAA0922

TLR2

RNF175

SFRP2

LRES region 13: chr4:154,082,585-154,930,678

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr4:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

184500000 185000000 185500000

4q35.1

ODZ3

DCTD

DCTD

FAM92A3

C4orf38

WWC2

CLDN22

CDKN2AIP

ING2

RWDD4A

C4orf41

C4orf41

STOX2

ENPP6

IRF2

CASP3

CASP3

CCDC111

MLF1IP

ACSL1

SLED1

LRES region 14: chr4:184,244,130-185,646,718

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr5:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

51000000 51500000 52000000 52500000 53000000 53500000

5q11.1

5q11.2

PARP8 ISL1 PELO

ITGA1

ITGA2

MOCS2

MOCS2

FST

FST

NDUFS4

ARL15

LRES region 15: chr5:50,713,715-53,015,925

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr5:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

64000000 65000000 66000000 67000000 68000000

5q12.1

5q12.2

5q12.3

5q13.1

HTR1A

RNF180

RNF180

RGS7BP

SFRS12IP1

SDCCAG10

ADAMTS6

CENPK

PPWD1

TRIM23

TRIM23

TRIM23

C5orf44

C5orf44

C5orf44

C5orf44

SGTB

NLN

ERBB2IP

ERBB2IP

SFRS12

SFRS12

MAST4

MAST4

CD180

PIK3R1

PIK3R1

PIK3R1

SLC30A5

SLC30A5

CCNB1

CENPH

MRPS36

CDK7

CCDC125

LRES region 16: chr5:63,496,427-67,638,162

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr5:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

110000000 111000000 112000000 113000000

5q21.3

5q22.1

5q22.2

5q22.3

MAN2A1 FLJ43080

SLC25A46

TSLP

TSLP

WDR36

CAMK4

STARD4

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf13

C5orf26

SNORA13

EPB41L4A

APC

APC

APC

SRP19

REEP5

DCP2

MCC

MCC

TSSK1B

YTHDC2

LRES region 17: chr5:109,931,047-112,876,763

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr6:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

55000000 55500000 56000000 56500000 57000000 57500000 58000000

6p12.1

6p11.2

FAM83B

HCRTR2

GFRAL

HMGCLL1

HMGCLL1

BMP5

COL21A1

DST

DST

DST

DST

BEND6

KIAA1586

ZNF451

ZNF451

BAG2

RAB23

RAB23

PRIM2

LRES region 18: chr6:55,146,009-57,622,335

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr6:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

85000000 86000000 87000000 88000000 89000000 90000000 91000000

q14.1

6q14.2

6q14.3

6q15

UBE2CBP

DOPEY1

PGM3

RWDD2A

ME1

PRSS35

SNAP91

C6orf159

CYB5R4

MRAP2

KIAA1009

TBX18 NT5E

SNX14

SNX14

SYNCRIP

SNHG5

SNORD50A

SNORD50B

HTR1E

CGA

ZNF292

GJB7

C6orf162

C6orf162

C6orf165

C6orf165

SLC35A1

RARS2

ORC3L

ORC3L

AKIRIN2

NCRNA00120

SPACA1

CNR1

CNR1

RNGTT

PNRC1

SRrp35

PM20D2

GABRR1

GABRR2

UBE2J1

RRAGD

ANKRD6

LYRM2

MDN1

CASP8AP2

CASP8AP2

CASP8AP2

GJA10

BACH2

LRES region 19: chr6:84,625,089-89,731,065

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr6:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

108000000 108500000

6q21

LOC553137

C6orf203

C6orf203

C6orf203

BEND3

PDSS2

SOBP

SCML4

SEC63

OSTM1

NR2E1

SNX3

LACE1

LRES region 20: chr6:107,579,454-108,690,157

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr6:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

112000000 112500000

6q21

SLC16A10

KIAA1919

REV3L

TRAF3IP2

TRAF3IP2

FYN

FYN

FYN

WISP3

WISP3

TUBE1

C6orf225

LAMA4

LAMA4

LAMA4

LAMA4

LAMA4

RFPL4B

LRES region 21: chr6:111,725,924-112,683,605

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr7:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

27000000 27500000 28000000

7p15.2

7p15.1

SKAP2 HOXA1

HOXA1

HOXA2

HOXA3

HOXA3

HOXA3

HOXA4

HOXA5

HOXA6

HOXA7

HOXA9

HOXA10

HOXA10

HOXA11

HOXA11AS

HOXA13

EVX1 HIBADH

TAX1BP1

TAX1BP1

JAZF1

LOC402644

CREB5

CREB5

CREB5

LRES region 22: chr7:27,096,595-28,187,962

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr7:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

98900000 99000000 99100000 99200000 99300000 99400000

7q22.1

ARPC1A

ARPC1B

PDAP1

BUD31

PTCD1

CPSF4

CPSF4

ATP5J2

ATP5J2

ATP5J2

ATP5J2

ZNF789

ZNF789

ZNF394

ZKSCAN5

ZKSCAN5

C7orf38

ZNF655

ZNF655

ZNF655

ZNF655

ZNF655

ZNF655

ZNF655

ZNF655

ZNF498

CYP3A5

CYP3A7

CYP3A4

CYP3A43

CYP3A43

CYP3A43

OR2AE1

TRIM4

TRIM4

GJC3

AZGP1

ZKSCAN1

LRES region 23: chr7:98,907,449-99,366,179

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr7:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

113000000 114000000 115000000 116000000 117000000 118000000

7q31.1

7q31.2

7q31.31

IFRD1

IFRD1

C7orf53

C7orf53

TMEM168

C7orf60

GPR85

LOC401397

LOC401397

PPP1R3A

FOXP2

FOXP2

FOXP2

MDFIC TFEC

TFEC

TES

TES

CAV2

CAV2

CAV1

MET

MET

CAPZA2

ST7OT1

ST7

ST7

ST7OT4

ST7OT2

ST7OT3

WNT2

WNT2

ASZ1

ASZ1

CFTR

CTTNBP2

LSM8

ANKRD7

ANKRD7

LRES region 24: chr7:112,245,438-116,363,646

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr8:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

11000000 11500000 12000000 12500000 13000000 13500000

8p23.1

8p22

SOX7

PINX1

XKR6

MTMR9

AMAC1L2

TDH

FAM167A

BLK

GATA4

NEIL2

NEIL2

NEIL2

NEIL2

FDFT1

CTSB

CTSB

CTSB

CTSB

CTSB

DEFB137

DEFB136

DEFB134

DEFB130

ZNF705D

LOC392196

DUB3

FAM86B1

FAM86B1

DEFB130

DEFB109P1

FAM86B2

LONRF1

LOC340357

C8orf79

C8orf79

DLC1

DLC1

DLC1

LRES region 25: chr8:11,177,927-13,417,767

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr8:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

106000000 107000000 108000000 109000000

8q22.3

8q23.1

RIMS2

RIMS2

TM7SF4

DPYS

LRP12

LRP12

ZFPM2 OXR1

OXR1

ABRA

ANGPT1

RSPO2

EIF3E

LRES region 26: chr8:105,459,828-108,580,459

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr9:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

500000 1000000 1500000 2000000 2500000

9p24.3

9p24.2

WASH1

FOXD4

CBWD1

C9orf66

DOCK8

KANK1

KANK1

DMRT1

DMRT3

DMRT2

DMRT2

DMRT2

SMARCA2

SMARCA2

FLJ35024

VLDLR

VLDLR

KCNV2

KIAA0020

LRES region 27: chr9:203,865-2,184,624

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr9:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

92500000 93000000 93500000 94000000

9q22.2

9q22.31

DIRAS2 SYK

SYK

SYK

SYK

AUH

NFIL3

ROR2

SPTLC1

SPTLC1

PTPRV

IARS

IARS

SNORA84

NOL8

NOL8

CENPP

OGN

OGN

OMD

LRES region 28: chr9:92,602,890-93,918,511

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr9:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

112500000 113000000 113500000

9q31.3

32

PALM2-AKAP2

PALM2-AKAP2

AKAP2

AKAP2

C9orf152

TXN

TXNDC8

SVEP1

MUSK

LPAR1

LPAR1

OR2K2

KIAA0368

ZNF483

ZNF483

PTGR1

DNAJC25

LOC552891

GNG10

C9orf84

C9orf84

UGCG

SUSD1

LRES region 29: chr9:112,155,785-113,598,354

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr10:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

86000000 86500000 87000000 87500000 88000000 88500000 89000000

10q23.1

10q23.2

GHITM

C10orf99

PCDH21

LRIT2

LRIT1

RGR

RGR

RGR

KIAA1128

GRID1

WAPAL

OPN4

OPN4

LDB3

LDB3

LDB3

LDB3

BMPR1A

MMRN2

SNCG

C10orf116

AGAP11

GLUD1

FAM35A

FAM22A

LOC728190

FAM22D

MINPP1

LRES region 30: chr10:86,074,898-88,721,652

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr10:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

123500000 124000000 124500000

10q26.12

10q26.13

FGFR2

FGFR2

ATE1

ATE1

NSMCE4A

TACC2

TACC2

TACC2

TACC2

BTBD16

PLEKHA1

PLEKHA1

ARMS2

HTRA1

DMBT1

DMBT1

DMBT1

C10orf120

FLJ46361

LRES region 31: chr10:123,205,637-124,265,414

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr11:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

12000000 12500000 13000000 13500000 14000000 14500000

11p15.3

11p15.2

GALNTL4

USP47

DKK3

DKK3

DKK3

MICAL2

MICALCL

PARVA

TEAD1

RASSF10

ARNTL

ARNTL

ARNTL

BTBD10

PTH

FAR1

SPON1

RRAS2

RRAS2

COPB1

PSMA1

PSMA1

PDE3B

LRES region 32: chr11:11,937,958-14,247,232

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr12:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

27000000 27500000

12p11.23

12p11.22

ITPR2

C12orf11

FGFR1OP2

TM7SF3

MED21

C12orf71

STK38L

ARNTL2

PPFIBP1

PPFIBP1

REP15

MRPS35

KLHDC5

LRES region 33: chr12:26,948,381-27,740,763

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr12:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

76000000 77000000 78000000 79000000

12q21.2

12q21.31

BBS10

OSBPL8

OSBPL8

ZDHHC17

CSRP2

E2F7

NAV3 SYT1

SYT1

SYT1

PAWR

PPP1R12A

MYF6

MYF5

LRES region 34: chr12:75,680,499-78,854,366

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr15:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

69000000 69500000 70000000 70500000

15q23

15q24.1

UACA

UACA

LARP6

LARP6

THAP10

LRRC49

LOC196993

THSD4

LOC645296

NR2E3

NR2E3

MYO9A

SENP8

GRAMD2

PKM2

PKM2

PKM2

PARP6

BRUNOL6

HEXA

TMEM202

ARIH1

GOLGA6B

HIGD2BP

BBS4

ADPGK

ADPGK

ADPGK

LRES region 35: chr15:68,901,948-70,472,322

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr16:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

54000000 54500000 55000000 55500000

16q12.2

16q13

IRX6 MMP2

MMP2

LPCAT2

CAPNS2

SLC6A2

CES4

CES1

CES1

CES1

CES7

GNAO1

GNAO1

AMFR

NUDT21

OGFOD1

BBS2

MT4

MT3

MT2A

MT1L

MT1E

MT1M

MT1A

MT1DP

MT1B

MT1F

MT1G

MT1H

MT1IP

MT1X

NUP93

SLC12A3

SLC12A3

SLC12A3

HERPUD1

HERPUD1

HERPUD1

CETP

LRES region 36: chr16:54,069,589-55,276,609

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr16:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

83000000 83500000

16q23.3

16q24.1

CDH13

HSBP1

MLYCD

OSGIN1

OSGIN1

OSGIN1

NECAB2

SLC38A8

MBTPS1

HSDL1

LRRC50

TAF1C

TAF1C

ADAD2

KCNG4

WFDC1

ATP2C2

KIAA1609

COTL1

KLHL36

USP10

CRISPLD2

ZDHHC7

KIAA0513

FAM92B

LRES region 37: chr16:82,643,869-83,686,337

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr17:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

36900000 36950000 37000000 37050000 37100000 37150000

17q21.2

KRT32

KRT35

KRT36

KRT13

KRT13

KRT15

KRT19

KRT9

KRT14

KRT16

KRT17

EIF1

GAST

HAP1

HAP1

HAP1

LRES region 38: chr17:36,909,759-37,102,424

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr18:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

9500000 10000000 10500000 11000000 11500000 12000000

18p11.22

18p11.21

ANKRD12

ANKRD12

TWSG1

RALBP1

PPP4R1

PPP4R1

RAB31

TXNDC2

TXNDC2

TXNDC2

VAPA

VAPA

APCDD1

NAPG

FAM38B

GNAL

GNAL

GNAL

CHMP1B

MPPE1

IMPA2

CIDEA

CIDEA

TUBB6

AFG3L2

SLMO1

SLMO1

SLMO1

SPIRE1

SPIRE1

SPIRE1

LRES region 39: chr18:9,697,228-11,899,779

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr18:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

59000000 60000000 61000000 62000000 63000000

18q21.33

18q22.1

KIAA1468

TNFRSF11A

ZCCHC2

PHLPP

BCL2

BCL2

KDSR

VPS4B

SERPINB5

SERPINB12

SERPINB13

SERPINB4

SERPINB3

SERPINB11

SERPINB7

SERPINB7

SERPINB2

SERPINB10

HMSD

SERPINB8

SERPINB8

SERPINB8

CDH7

CDH7

CDH19

LRES region 40: chr18:58,940,559-62,423,389

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr22:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

31000000 31500000 32000000 32500000 33000000

22q12.3

LOC402057

SLC5A1

LOC150297

RFPL2

RFPL2

SLC5A4

RFPL3

RFPL3

RFPL3S

RFPL3S

C22orf28

BPIL2

FBXO7

FBXO7

SYN3

SYN3

SYN3

TIMP3 LARGE

LARGE

LRES region 41: chr22:31,112,563-32,647,410

RefSeq genes:

On

co

min

e




exp1 / exp2:










chr22:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

37800000 37900000 38000000 38100000 38200000

22q13.1

APOBEC3A

APOBEC3B

APOBEC3C

APOBEC3D

APOBEC3F

APOBEC3F

APOBEC3G

APOBEC3H

CBX7 PDGFB

PDGFB

RPL3

RPL3

SNORD83B

SNORD83A

RNU86

SNORD43

SYNGR1

SYNGR1

SYNGR1

MAP3K7IP1

MAP3K7IP1

MGAT3

LRES region 42: chr22:37,739,208-38,112,526

RefSeq genes:

On

co

min

e




exp1 / exp2:










chrX:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

8500000 9000000 9500000 10000000 10500000 11000000 11500000

Xp22.31

Xp22.2

VCX

PNPLA4

PNPLA4

VCX2

VCX3B

KAL1

FAM9A

FAM9B

TBL1X

TBL1X

TBL1X

TBL1X

GPR143

SHROOM2

WWC3

CLCN4

MID1

MID1

MID1

HCCS

HCCS

ARHGAP6

ARHGAP6

ARHGAP6

AMELX

AMELX

AMELX

MSL3

MSL3

MSL3

MSL3

LRES region 43: chrX:8,391,871-11,229,802

RefSeq genes:

On

co

min

e




exp1 / exp2:










chrX:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

37500000 38000000 38500000

Xp21.1

Xp11.4

PRRG1

PRRG1

LANCL3

XK

CYBB

DYNLT3

CXorf27

SYTL5

SRPX

RPGR

RPGR

OTC

TSPAN7

MID1IP1

MID1IP1

MID1IP1

LRES region 44: chrX:37,428,928-38,434,118

RefSeq genes:

On

co

min

e




exp1 / exp2:










chrX:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

102000000 102500000 103000000

Xq22.1

Xq22.2

NXF2B

NXF2

NXF2

TMSL8

NXF4

ARMCX5

GPRASP1

GPRASP1

GPRASP1

GPRASP2

GPRASP2

BHLHB9

RAB40AL

BEX1

NXF3

BEX4

BEX4

TCEAL8

TCEAL8

TCEAL5

BEX2

TCEAL7

WBP5

WBP5

WBP5

WBP5

NGFRAP1

NGFRAP1

NGFRAP1

RAB40A

TCEAL4

TCEAL4

TCEAL4

TCEAL4

TCEAL3

TCEAL3

TCEAL1

TCEAL1

TCEAL1

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

MORF4L2

GLRA4

TMEM31

PLP1

PLP1

PLP1

RAB9B

MGC39900

H2BFXP

H2BFWT

H2BFXP

MCART6

LRES region 45: chrX:101,791,973-102,974,838

RefSeq genes:

On

co

min

e




exp1 / exp2:










chrX:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

107000000 107500000 108000000 108500000 109000000

Xq22.3

CXorf41 PRPS1

TSC22D3

TSC22D3

TSC22D3

MID2

MID2

TEX13B

VSIG1

PSMD10

PSMD10

ATG4A

ATG4A

COL4A6

COL4A6

COL4A5

COL4A5

COL4A5

IRS4

GUCY2F

NXT2

KCNE1L

ACSL4

ACSL4

TMEM164

AMMECR1

AMMECR1

SNORD96B

LRES region 46: chrX:106,842,107-108,864,277

RefSeq genes:

On

co

min

e




exp1 / exp2:










chrX:LRES

exp1:13T/13N

exp2:7T/6N

LaPointe:62T/41N

Singh:52T/50N


Yu:64T/23N

Tomlins:30T/22N


Welsh:25T/9N

Luo:16T/9N

Vanaja:27T/8N

LNCaP+Aza

PC3+Aza

DU145+Aza

MDA2A+Aza

CpG Islands

134000000 134500000 135000000 135500000

Xq26.3

FAM122B

FAM122C

MOSPD1

FAM127C

FAM127A

FAM127B

FAM127B

NCRNA00087

CXorf48

CXorf48

ZNF75D

ZNF449

NCRNA00086

DDX26B

CT45-1

CT45-4

CT45-2

CT45-3

CT45-4

CT45-5

CT45-6

SAGE1

MMGT1

SLC9A6

SLC9A6

FHL1

MAP7D3

GPR112

BRS3

HTATSF1

VGLL1

CD40LG

ARHGEF6

LRES region 47: chrX:133,993,062-135,423,171

RefSeq genes:

On

co

min

e




exp1 / exp2:










2: additional support for lres using oncomine data sets. · additional file 2: additional support...

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