Methods and molecular pharmacodynamic biomarkers for multiple signaling pathways in response to carboxyamidotriazole orotate

1. A method for quantifying the response to carboxyamidotriazole orotate (CTO) on more than one signature pathway wherein said signature pathways are RAS, GFS, MEKi, HDAC, NOTCH, WNTβ-catenin, HSP90, EGFR, p53, EGR1, CEACAMI, TGFβ or Dystonin and on pharmacodynamic biomarkers for each of said signature pathways, said method comprising:

a) obtaining a cell sample obtained from a subject and treating cultures of the cell sample with varying doses of CTO alone, and maintaining the cultures for different time periods;

b) isolating the mRNA from the treated cultures of the cell sample obtained in step a), and preparing representative cDNA therefrom, and measuring the transcriptional alteration in expression in the treated cultures of the cell sample;

c) calculating a signature score for each of the pharmacodynamics biomarkers of each of said signature pathways using the Ingenuity Pathway Analysis (IPA) System and quantitating the response to the varying doses of CTO, and selecting a list of overlapping genes expressing after 8 hours and 24 hours of exposure to CTO based on the calculated signature scores, from the list consisting of:

Probeset ID

Entrez Gene

Gene Symbol

222450_at

56937

PMEPA1

233565_s_at

100528031///27111

FKBP1A-SDCBP2///

SDCBP2

242832_at

5187

PER1

240463_at

—

—

213039_at

23370

ARHGEF18

235072_s_at

63971

KIF13A

208926_at

4758

NEU1

237444_at

—

—

239451_at

—

—

222288_at

—

—

227579_at

2241

FER

212717_at

9842

PLEKHM1

226853_at

55589

BMP2K

214112_s_at

541578///91966

CXorf40A///

CXorf40B

209012_at

7204

TRIO

219476_at

79098

C1orf116

238086_at

100129617

LOC100129617

230721_at

730094

C16orf52

1566079_at

647190

RPS16P5

223839_s_at

6319

SCD

225671_at

124976

SPNS2

212961_x_at

541578

CXorf40B

223659_at

84000

TMPRSS13

229909_at

283358

B4GALNT3

223467_at

51655

RASD1

235146_at

57458

TMCC3

235548_at

164284

APCDD1L

206816_s_at

26206

SPAG8

242323_at

81579

PLA2G12A

224579_at

81539

SLC38A1

213315_x_at

91966

CXorf40A

227314_at

3673

ITGA2

227093_at

57602

USP36

200760_s_at

10550

ARL6IP5

201790_s_at

1717

DHCR7

1554980_a_at

467

ATF3

242255_at

22884

WDR37

219267_at

51228

GLTP

1555786_s_at

645687

LINC00520

229734_at

283174

LOC283174

242856_at

—

—

201037_at

5214

PFKP

1562970_at

—

—

201465_s_at

3725

JUN

202067_s_at

3949

LDLR

223679_at

1499

CTNNB1

201235_s_at

7832

BTG2

225662_at

51776

ZAK

204401_at

3783

KCNN4

222906_at

28982

FLVCR1

238613_at

51776

ZAK

206414_s_at

8853

ASAP2

210794_s_at

55384

MEG3

226621_at

9180

OSMR

230682_x_at

8714

ABCC3

235668_at

639

PRDM1

205483_s_at

9636

ISG15

215808_at

5655

KLK10

212281_s_at

27346

TMEM97

212282_at

27346

TMEM97

226287_at

91057

CCDC34

213618_at

116984

ARAP2

231089_at

100505664

LOC100505664

227140_at

3624

INHBA

231467_at

—

—

202967_at

2941

GSTA4

230323_s_at

120224

TMEM45B

224471_s_at

8945

BTRC

202708_s_at

8349

HIST2H2BE

242871_at

54852

PAQR5

205627_at

978

CDA

235542_at

200424

TET3

240410_at

—

—

236656_s_at

100288911

LOC100288911

206164_at

9635

CLCA2

203159_at

2744

GLS

224991_at

80790

CMIP

204258_at

1105

CHD1

228249_at

119710

C11orf74

229013_at

145783

LOC145783

211547_s_at

5048

PAFAH1B1

226863_at

642273

FAM110C

208161_s_at

8714

ABCC3

214805_at

1973

ElF4A1

229429_x_at

728855///728875

LOC728855///

LOC728875

202720_at

26136

TES

224995_at

56907

SPIRE1

214771_x_at

23164

MPRIP

201939_at

10769

PLK2

238587_at

84959

UBASH3B

232113_at

—

—

208690_s_at

9124

PDLIM1

201464_x_at

3725

JUN

236657_at

100288911

LOC100288911

215541_s_at

1729

DIAPH1

238028_at

647024

C6orf132

226893_at

27

ABL2

237576_x_at

100506480

LOC100506480

1552256_a_at

949

SCARB1

215255_at

22997

IGSF9B

1557258_a_at

8915

BCL10

240623_at

—

—

228754_at

6533

SLC6A6

217257_at

6452

SH3BP2

241036_at

—

—

242553_at

8714

ABCC3

239358_at

—

—

210868_s_at

79071

ELOVL6

200815_s_at

5048

PAFAH1B1

208436_s_at

3665

IRF7

208138_at

2520

GAST

241780_at

—

—

200730_s_at

7803

PTP4A1

219697_at

9956

HS3ST2

201693_s_at

1958

EGR1

218847_at

10644

IGF2BP2

230469_at

219790

RTKN2

209917_s_at

11257

TP53TG1

224329_s_at

84518

CNFN

212253_x_at

100652766///667

DST///

LOC100652766

238058_at

150381

LOC150381

239334_at

57488

ESYT2

222271_at

—

—

216718_at

388699

LINC00302

219076_s_at

5827

PXMP2

204475_at

4312

MMP1

221185_s_at

84223

IQCG

203586_s_at

379

ARL4D

217802_s_at

64710

NUCKS1

205767_at

2069

EREG

228360_at

130576

LYPD6B

228917_at

—

—

228748_at

966

CD59

219632_s_at

23729///7442

SHPK///TRPV1

238715_at

646014

LOC646014

218810_at

80149

ZC3H12A

225177_at

80223

RAB11FIP1

224454_at

55500

ETNK1

209498_at

634

CEACAM1

1557257_at

8915

BCL10

225133_at

51274

KLF3

202340_x_at

3164

NR4A1

1556545_at

—

—

212474_at

23080

AVL9

210241_s_at

11257

TP53TG1

243543_at

—

—

239132_at

4842

NOS1

222757_s_at

51776

ZAK

201194_at

6415

SEPW1

229874_x_at

100506687

LOC100506687

202557_at

6782

HSPA13

239669_at

—

—

231907_at

27

ABL2

229074_at

30844

EHD4

205428_s_at

794

CALB2

205822_s_at

3157

HMGCS1

210869_s_at

4162

MCAM

225665_at

51776

ZAK

212781_at

5930

RBBP6

232355_at

767579

SNORD114-3

213288_at

129642

MBOAT2

221666_s_at

29108

PYCARD

203072_at

4643

MYO1E

215465_at

26154

ABCA12

224453_s_at

55500

ETNK1

216935_at

388699

LINC00302

209086_x_at

4162

MCAM

218833_at

51776

ZAK

209377_s_at

9324

HMGN3

223519_at

51776

ZAK

210138_at

8601

RGS20

1558845_at

100506089

LOC100506089

201819_at

949

SCARB1

204310_s_at

4882

NPR2

239377_at

84285

EIF1AD

224611_s_at

80331

DNAJC5

219155_at

26207

PITPNC1

227163_at

119391

GSTO2

209633_at

5523

PPP2R3A

219681_s_at

80223

RAB11FIP1

221860_at

3191

HNRNPL

243296_at

10135

NAMPT

237133_at

—

—

1556000_s_at

55727

BTBD7

204681_s_at

9771

RAPGEF5

215726_s_at

1528

CYB5A

210886_x_at

11257

TP53TG1

226597_at

92840

REEP6

204995_at

8851

CDK5R1

236119_s_at

6706

SPRR2G

219228_at

55422

ZNF331

234971_x_at

113026

PLCD3

201127_s_at

47

ACLY

226880_at

64710

NUCKS1

209383_at

1649

DDIT3

204168_at

4258

MGST2

239670_at

65268

WNK2

208512_s_at

4301

MLLT4

213281_at

3725

JUN

218310_at

154881///27342

KCTD7///RABGEF1

205151_s_at

9865

TRIL

218217_at

59342

SCPEP1

205055_at

3682

ITGAE

215009_s_at

100499177

THAP9-AS1

227484_at

57522

SRGAP1

239769_at

1009

CDH11

230360_at

342035

GLDN

227112_at

23023

TMCC1

201482_at

5768

QS0X1

210337_s_at

47

ACLY

203911_at

5909

RAP1GAP

206683_at

7718

ZNF165

202935_s_at

6662

SOX9

218951_s_at

55344

PLCXD1

233488_at

84659

RNASE7

202562_s_at

11161

C14orf1

208745_at

10632

ATP5L

236078_at

57707

KIAA1609

226226_at

120224

TMEM45B

213854_at

9145

SYNGR1

243955_at

—

—

222111_at

54629

FAM63B

1560296_at

—

—

240038_at

—

—

211372_s_at

7850

IL1R2

202672_s_at

467

ATF3

218717_s_at

55214

LEPREL1

228366_at

—

—

230516_at

115416

MALSU1

201920_at

6574

SLC20A1

209632_at

5523

PPP2R3A

207367_at

479

ATP12A

1557256_a_at

—

—

200811_at

1153

CIRBP

205201_at

2737

GLI3

227724_at

728190

LOC728190

205403_at

7850

IL1R2

242827_x_at

—

—

228084_at

81579

PLA2G12A

209365_s_at

1893

ECM1

243279_at

—

—

224946_s_at

84317

CCDC115

218708_at

29107

NXT1

1560531_at

353132

LCE1B

207761_s_at

25840

METTL7A

206011_at

834

CASP1

213703_at

150759

LINC00342

224595_at

23446

SLC44A1

224613_s_at

80331

DNAJC5

212504_at

22982

DIP2C

213682_at

10762

NUP50

205247_at

4855

NOTCH4

228235_at

84848

MGC16121

242873_at

—

—

205960_at

5166

PDK4

230494_at

6574

SLC20A1

221260_s_at

81566

CSRNP2

224480_s_at

84803

AGPAT9

210180_s_at

6434

TRA2B

204621_s_at

4929

NR4A2

217863_at

8554

PIAS1

236423_at

—

—

223421_at

50626

CYHR1

220272_at

54796

BNC2

201791_s_at

1717

DHCR7

215574_at

—

—

224328_s_at

84648

LCE3D

211828_s_at

23043

TNIK

58367_s_at

79744

ZNF419

218950_at

64411

ARAP3

1552703_s_at

114769///834

CARD16///CASP1

219687_at

55733

HHAT

232127_at

1184

CLCN5

218377_s_at

10069

RWDD2B

210335_at

9182

RASSF9

227927_at

—

—

227224_at

55103

RALGPS2

224778_s_at

57551

TAOK1

229566_at

645638

LOC645638

202734_at

9322

TRIP10

201851_at

6455

SH3GL1

237337_at

—

—

37152_at

5467

PPARD

209687_at

6387

CXCL12

203152_at

64976

MRPL40

201627_s_at

3638

INSIG1

232593_at

93082

NEURL3

224769_at

57551

TAOK1

209702_at

79068

FTO

204546_at

9764

KIAA0513

232224_at

5648

MASP1

239930_at

2590

GALNT2

203178_at

2628

GATM

235782_at

—

—

218181_s_at

9448

MAP4K4

233520_s_at

202333

CMYA5

213456_at

25928

SOSTDC1

219528_s_at

64919

BCL11B

224945_at

55727

BTBD7

214866_at

5329

PLAUR

209941_at

8737

RIPK1

226029_at

57216

VANGL2

212596_s_at

10042

HMGXB4

229873_at

283219

KCTD21

226392_at

5922

RASA2

226005_at

7326

UBE2G1

214445_at

22936

ELL2

227680_at

284695

ZNF326

227786_at

90390

MED30

222067_x_at

3017

HIST1H2BD

1569106_s_at

55209

SETD5

231785_at

4909

NTF4

223937_at

27086

FOXP1

1558685_a_at

158960

LOC158960

211965_at

677

ZFP36L1

39549_at

4862

NPAS2

203800_s_at

63931

MRPS14

1556321_a_at

—

—

212321_at

8879

SGPL1

222154_s_at

26010

SPATS2L

218774_at

28960

DCPS

212268_at

1992

SERPINB1

213134_x_at

10950

BTG3

230669_at

5922

RASA2

1559901_s_at

388815

LINC00478

225298_at

25953

PNKD

242558_at

—

—

226043_at

26086

GPSM1

210236_at

8500

PPFIA1

214066_x_at

4882

NPR2

240024_at

23541

SEC14L2

235462_at

132864

CPEB2

1554015_a_at

1106

CHD2

235347_at

84859

LRCH3

230847_at

56897

WRNIP1

201427_s_at

6414

SEPP1

1557905_s_at

960

CD44

219084_at

64324

NSD1

206176_at

654

BMP6

219826_at

79744

ZNF419

212356_at

23351

KHNYN

218909_at

26750

RPS6KC1

230555_s_at

90390

MED30

212687_at

3987

LIMS1

203098_at

9425

CDYL

229054_at

677

ZFP36L1

236039_at

284348

LYPD5

209661_at

3801

KIFC3

209560_s_at

8788

DLK1

225812_at

619208

C6orf225

227829_at

120071

GYLTL1B

238623_at

—

—

229415_at

54205

CYCS

209222_s_at

9885

OSBPL2

1555809_at

83716

CRISPLD2

204567_s_at

9619

ABCG1

232277_at

64078

SLC28A3

237197_at

—

—

225209_s_at

118424

UBE2J2

231916_at

4842

NOS1

212279_at

27346

TMEM97

204862_s_at

4832

NME3

230483_at

—

—

212856_at

23151

GRAMD4

224650_at

114569

MAL2

202963_at

5993

RFX5

225320_at

90550

MCU

236274_at

8662

ElF3B

209780_at

57157

PHTF2

218823_s_at

54793

KCTD9

227787_s_at

90390

MED30

230296_at

730094

C16orf52

222892_s_at

55287

TMEM40

210610_at

634

CEACAM1

230031_at

3309

HSPA5

238477_at

10749

KIF1C

209409_at

2887

GRB10

217995_at

58472

SQRDL

226873_at

54629

FAM63B

1553722_s_at

220441

RNF152

204710_s_at

26100

WIPI2

212653_s_at

23301

EHBP1

203979_at

1593

CYP27A1

244350_at

4651

MYO10

223233_s_at

57530

CGN

1555967_at

—

—

214355_x_at

100128553///

CTAGE15P///

100142659///340307///

CTAGE4///

441294///643854

CTAGE6P///

CTAGE8///CTAGE9

214469_at

3012///8335

HIST1H2AB///

HIST1H2AE

212472_at

9645

MICAL2

228115_at

64762

FAM59A

228964_at

639

PRDM1

230027_s_at

84545

MRPL43

207318_s_at

8621

CDK13

221689_s_at

51227

PIGP

219270_at

79094

CHAC1

225299_at

4645

MYO5B

239770_at

83850

ESYT3

226399_at

79982

DNAJB14

226656_at

10491

CRTAP

228852_at

2029

ENSA

206239_s_at

6690

SPINK1

210993_s_at

4086

SMAD1

238462_at

84959

UBASH3B

211962_s_at

677

ZFP36L1

224666_at

197370

NSMCE1

239028_at

130574

LYPD6

213577_at

6713

SQLE

202011_at

7082

TJP1

212254_s_at

100652766///667

DST///

LOC100652766

221701_s_at

64220

STRA6

239576_at

57509

MTUS1

234418_x_at

960

CD44

227985_at

100506098

LOC100506098

213462_at

4862

NPAS2

224975_at

4774

NFIA

225990_at

91653

BOC

240616_at

—

—

219911_s_at

28231

SLCO4A1

224970_at

4774

NFIA

214623_at

26226

FBXW4P1

239478_x_at

55668

C14orf118

226909_at

85460

ZNF518B

208670_s_at

23741

EID1

206192_at

1041

CDSN

222173_s_at

55357

TBC1D2

228450_at

144100

PLEKHA7

1558097_at

253143

PRR14L

219373_at

54344

DPM3

230388_s_at

644246

KANSL1-AS1

207098_s_at

55669

MFN1

223484_at

84419

C15orf48

244804_at

8878

SQSTM1

229679_at

400073

C12orf76

225826_at

326625

MMAB

213352_at

23023

TMCC1

211883_x_at

634

CEACAM1

210387_at

8339///8343///8344///

HIST1H2BC///

8346///8347

HIST1H2BE///

HIST1H2BF///

HIST1H2BG///

HIST1H2BI

210916_s_at

960

CD44

221432_s_at

81894

SLC25A28

218487_at

210

ALAD

223264_at

59274

MESDC1

206356_s_at

2774

GNAL

218097_s_at

79004

CUEDC2

228001_at

757

TMEM5OB

212441_at

9778

K1AA0232

201854_s_at

23300

ATMIN

121_at

7849

PAX8

222143_s_at

64419

MTMR14

1558002_at

11171

STRAP

226040_at

—

—

226141_at

91050

CCDC149

1556567_at

4676

NAP1L4

226263_at

154007

SNRNP48

212074_at

23353

SUN1

227387_at

54780

NSMCE4A

232795_at

—

—

203936_s_at

4318

MMP9

225033_at

6482

ST3GAL1

209109_s_at

7105

TSPAN6

213351_s_at

23023

TMCC1

203047_at

6793

STK10

220721_at

80110

ZNF614

1556127_at

23181

DIP2A

215016_x_at

100652766///667

DST///

LOC100652766

206576_s_at

634

CEACAM1

240674_at

3720

JARID2

225646_at

1075

CTSC

1554010_at

3340

NDST1

204100_at

7067

THRA

221840_at

5791

PTPRE

209078_s_at

25828

TXN2

218530_at

29109

FHOD1

235434_at

—

—

230063_at

9422

ZNF264

40420_at

6793

STK10

221027_s_at

81579

PLA2G12A

244202_at

—

—

212108_at

23197

FAF2

204294_at

275

AMT

225503_at

207063

DHRSX

212810_s_at

6509

SLC1A4

214814_at

91746

YTHDC1

228468_at

84930

MASTL

209108_at

7105

TSPAN6

220444_at

79230

ZNF557

206172_at

3598

IL13RA2

225002_s_at

25870

SUMF2

212205_at

94239

H2AFV

228851_s_at

2029

ENSA

209048_s_at

23613

ZMYND8

211846_s_at

5818

PVRL1

238909_at

6281

S100A10

205503_at

5784

PTPN14

243829_at

673

BRAF

244379_at

—

—

223251_s_at

55608

ANKRD10

202633_at

11073

TOPBP1

214502_at

8970

HIST1H2BJ

221773_at

2004

ELK3

41858_at

27315

PGAP2

212850_s_at

4038

LRP4

223408_s_at

—

—

214472_at

3013///8350///8351///

HIST1H2AD///

8352///8353///8354///

HIST1H3A///

8355///8356///8357

HIST1H3B///

8358/

HIST1H3C///

HIST1H3D///

HIST1H3E///

HIST1H3F///

HIST1H3G///

HIST1H3H///

HIST1H3I///

HIST1H3J

225647_s_at

1075

CTSC

1559977_a_at

284723

SLC25A34

211347_at

8555

CDC14B

1558208_at

—

—

227570_at

144110

TMEM86A

227492_at

100506658///647859

LOC647859///OCLN

1558778_s_at

57496

MKL2

31637_s_at

7067///9572

NR1D1///THRA

229190_at

100507376

LOC100507376

236188_s_at

4676

NAP1L4

212503_s_at

22982

DIP2C

204760_s_at

7067///9572

NR1D1///THRA

212099_at

388

RHOB

214873_at

91355

LRP5L

228181_at

7779

SLC30A1

212763_at

23271

CAMSAP2

226285_at

4076

CAPRIN1

213567_at

3840

KPNA4

203927_at

4794

NFKBIE

208523_x_at

8339///8343///8344///

HIST1H2BC///

8346///8347

HIST1H2BE///

HIST1H2BF///

HIST1H2BG///

HIST1H2BI

219389_at

55061

SUSD4

202329_at

1445

CSK

238523_at

79786

KLHL36

1565016_at

3276

PRMT1

226409_at

128637

TBC1D20

229926_at

100500850

MIR3682

208527_x_at

8339///8343///8344///

HIST1H2BC///

8346///8347

HIST1H2BE///

HIST1H2BF///

HIST1H2BG///

HIST1H2BI

223598_at

5887

RAD23B

243797_at

9262

STK17B

203317_at

23550

PSD4

230965_at

9099

USP2

208490_x_at

8339///8343///8344///

HIST1H2BC///

8346///8347

HIST1H2BE///

HIST1H2BF///

HIST1H2BG///

HIST1H2BI

235514_at

151516

ASPRV1

209098_s_at

182

JAG1

1554229_at

153222

CREBRF

209398_at

3006

HIST1H1C

202629_at

10513

APPBP2

203428_s_at

25842

ASF1A

238005_s_at

25942

SIN3A

214455_at

8339///8343///8344///

HIST1H2BC///

8346///8347

HIST1H2BE///

HIST1H2BF///

HIST1H2BG///

HIST1H2BI

214073_at

2017

CTTN

203140_at

604

BCL6

232150_at

—

—

208546_x_at

8345

HIST1H2BH

243446_at

84962

AJUBA

236207_at

6744

SSFA2

212016_s_at

5725

PTBP1

232311_at

567

B2M

219711_at

54807

ZNF586

208579_x_at

54145///85236

H2BFS///

HIST1H2BK

239493_at

6129

RPL7

214074_s_at

2017

CTTN

228091_at

55014

STX17

234331_s_at

151354

FAM84A

212372_at

4628

MYH10

Probeset ID

Gene Title

222450_at

prostate transmembrane

protein, androgen induced 1

233565_s_at

FKBP1A-SDCBP2 readthrough

(non-protein coding)///

syndecan binding protein

(syntenin)

242832_at

period homolog 1 (Drosophila)

240463_at

—

213039_at

Rho/Rac guanine nucleotide

exchange factor (GEF) 18

235072_s_at

kinesin family member 13A

208926_at

sialidase 1 (lysosomal

sialidase)

237444_at

—

239451_at

—

222288_at

—

227579_at

fer (fps/fes related) tyrosine

kinase

212717_at

pleckstrin homology domain

containing, family M (with RUN

domain) member 1

226853_at

BMP2 inducible kinase

214112_s_at

chromosome X open reading

frame 40A///chromosome X

open reading frame 40B

209012_at

triple functional domain (PTPRF

interacting)

219476_at

chromosome 1 open reading

frame 116

238086_at

uncharacterized

LOC100129617

230721_at

chromosome 16 open reading

frame 52

1566079_at

ribosomal protein S16

pseudogene 5

223839_s_at

stearoyl-CoA desaturase (delta-

9-desaturase)

225671_at

spinster homolog 2 (Drosophila)

212961_x_at

chromosome X open reading

frame 40B

223659_at

transmembrane protease,

serine 13

229909_at

beta-1,4-N-acetyl-galactosaminyl

223467_at

transferase 3 RAS, dexamethasone-

induced 1

235146_at

transmembrane and coiled-coil

domain family 3

235548_at

adenomatosis polyposis coli

down-regulated 1-like

206816_s_at

sperm associated antigen 8

242323_at

phospholipase A2, group XIIA

224579_at

solute carrier family 38,

member 1

213315_x_at

chromosome X open reading

frame 40A

227314_at

integrin, alpha 2 (CD49B, alpha

2 subunit of VLA-2 receptor)

227093_at

Ubiquitin specific peptidase 36

200760_s_at

ADP-ribosylation-like factor 6

interacting protein 5

201790_s_at

7-dehydrocholesterol reductase

1554980_a_at

activating transcription factor 3

242255_at

WD repeat domain 37

219267_at

glycolipid transfer protein

1555786_s_at

long intergenic non-protein

coding RNA 520

229734_at

uncharacterized LOC283174

242856_at

—

201037_at

phosphofructokinase, platelet

1562970_at

—

201465_s_at

jun proto-oncogene

202067_s_at

low density lipoprotein receptor

223679_at

catenin (cadherin-associated

protein), beta 1, 88kDa

201235_s_at

BTG family, member 2

225662_at

sterile alpha motif and leucine

zipper containing kinase AZK

potassium intermediate/small

204401_at

conductance calcium-activated

channel, subfamily N, member

222906_at

feline leukemia virus subgroup

C cellular receptor 1

238613_at

sterile alpha motif and leucine

zipper containing kinase AZK

ArfGAP with SH3 domain,

206414_s_at

ankyrin repeat and PH domain

2

210794_s_at

maternally expressed 3 (non-protein

coding)

226621_at

oncostatin M receptor

230682_x_at

ATP-binding cassette, sub-family C

(CFTR/MRP), member3

235668_at

PR domain containing 1, with

ZNF domain

205483_s_at

ISG15 ubiquitin-like modifier

215808_at

kallikrein-related peptidase 10

212281_s_at

transmembrane protein 97

212282_at

transmembrane protein 97

226287_at

coiled-coil domain containing 34

213618_at

ArfGAP with RhoGAP domain,

ankyrin repeat and PH domain

2

231089_at

uncharacterized

LOC100505664

227140_at

inhibin, beta A

231467_at

—

202967_at

glutathione S-transferase alpha

4

230323_s_at

transmembrane protein 45B

224471_s_at

beta-transducin repeat

containing E3 ubiquitin protein

ligase

202708_s_at

histone cluster 2, H2be

242871_at

progestin and adipoQ receptor

family member V

205627_at

cytidine deaminase

235542_at

tet methylcytosine dioxygenase

3

240410_at

—

236656_s_at

uncharacterized

LOC100288911

206164_at

chloride channel accessory 2

203159_at

glutaminase

224991_at

c-Maf inducing protein

204258_at

chromodomain helicase DNA

binding protein 1

228249_at

chromosome 11 open reading

frame 74

229013_at

uncharacterized LOC145783

platelet-activating factor

211547_s_at

acetylhydrolase lb, regulatory

subunit 1 (45kDa)

226863_at

family with sequence similarity

110, member C

208161_s_at

ATP-binding cassette, sub-

family C (CFTR/MRP), member 3

214805_at

eukaryotic translation initiation

factor 4A1

229429_x_at

uncharacterized LOC728855///

uncharacterized LOC728875

202720_at

testis derived transcript (3 LIM

domains)

224995_at

spire homolog 1 (Drosophila)

214771_x_at

myosin phosphatase Rho

interacting protein

201939_at

polo-like kinase 2

238587_at

ubiquitin associated and SH3

domain containing B

232113_at

—

208690_s_at

PDZ and LIM domain 1

201464_x_at

jun proto-oncogene

236657_at

uncharacterized

LOC100288911

215541_s_at

diaphanous homolog 1

(Drosophila)

238028_at

chromosome 6 open reading

frame 132

226893_at

v-abl Abelson murine leukemia

viral oncogene homolog 2

237576_x_at

uncharacterized

LOC100506480

1552256_a_at

scavenger receptor class B,

member 1

215255_at

immunoglobulin superfamily,

member 9B

1557258_a_at

B-cell CLL/lymphoma 10

240623_at

—

solute carrier family 6

228754_at

(neurotransmitter transporter,

taurine), member 6

217257_at

SH3-domain binding protein 2

241036_at

—

242553_at

ATP-binding cassette, sub-

family C (CFTR/MRP), member 3

239358_at

—

210868_s_at

ELOVL fatty acid elongase 6

platelet-activating factor

200815_s_at

acetylhydrolase lb, regulatory

subunit 1 (45kDa)

208436_s_at

interferon regulatory factor 7

208138_at

gastrin

241780_at

—

200730_s_at

protein tyrosine phosphatase

type IVA, member 1

219697_at

heparan sulfate (glucosamine)

3-0-sulfotransferase 2

201693_s_at

early growth response 1

218847_at

insulin-like growth factor 2

mRNA binding protein 2

230469_at

rhotekin 2

209917_s_at

TP53 target 1 (non-protein

coding)

224329_s_at

cornifelin

212253_x_at

dystonin///dystonin-like

238058_at

uncharacterized LOC150381

239334_at

Extended synaptotagmin-like

protein 2

222271_at

—

216718_at

long intergenic non-protein

coding RNA 302

219076_s_at

peroxisomal membrane protein

2, 22kDa

204475_at

matrix metallopeptidase 1

(interstitial collagenase)

221185_s_at

IQ motif containing G

203586_s_at

ADP-ribosylation factor-like 4D

nuclear casein kinase and

217802_s_at

cyclin-dependent kinase

substrate 1

205767_at

epiregulin

228360_at

LY6/PLAUR domain containing

6B

228917_at

—

228748_at

CD59 molecule, complement

regulatory protein

219632_s_at

sedoheptulokinase///transient

receptor potential cation

channel, subfamily V, member

238715_at

Uncharacterized LOC646014

218810_at

zinc finger CCCH-type

containing 12A

225177_at

RAB11 family interacting

protein 1 (class I)

224454_at

ethanolamine kinase 1

209498_at

carcinoembryonic antigen-

related cell adhesion molecule

1 (biliary glycoprotein)

1557257_at

B-cell CLL/lymphoma 10

225133_at

Kruppel-like factor 3 (basic)

202340_x_at

nuclear receptor subfamily 4,

group A, member 1

1556545_at

—

212474_at

AVL9 homolog (S. cerevisiase)

210241_s_at

TP53 target 1 (non-protein

coding)

243543_at

—

239132_at

nitric oxide synthase 1

(neuronal)

222757_s_at

sterile alpha motif and leucine

zipper containing kinase AZK

201194_at

selenoprotein W, 1

229874_x_at

uncharacterized

LOC100506687

202557_at

heat shock protein 70kDa

family, member 13

239669_at

—

231907_at

v-abl Abelson murine leukemia

viral oncogene homolog 2

229074_at

EH-domain containing 4

205428_s_at

calbindin 2

205822_s_at

3-hydroxy-3-methylglutaryl-CoA

synthase 1 (soluble)

210869_s_at

melanoma cell adhesion

molecule

225665_at

sterile alpha motif and leucine

zipper containing kinase AZK

212781_at

retinoblastoma binding protein

6

232355_at

small nucleolar RNA, C/D box

114-3

213288_at

membrane bound 0-acyltransferase

domain containing 2

221666_s_at

PYD and CARD domain

containing

203072_at

myosin IE

215465_at

ATP-binding cassette, sub-family A

(ABC1), member 12

224453_s_at

ethanolamine kinase 1

216935_at

long intergenic non-protein

coding RNA 302

209086_x_at

melanoma cell adhesion

molecule

218833_at

sterile alpha motif and leucine

zipper containing kinase AZK

209377_s_at

high mobility group

nucleosomal binding domain 3

223519_at

sterile alpha motif and leucine

zipper containing kinase AZK

210138_at

regulator of G-protein signaling

20

1558845_at

uncharacterized

LOC100506089

201819_at

scavenger receptor class B,

member 1

204310_s_at

natriuretic peptide receptor

B/guanylate cyclase B

(atrionatriuretic peptide

receptor B

239377_at

eukaryotic translation initiation

factor 1A domain containing

224611_s_at

DnaJ (Hsp40) homolog,

subfamily C, member 5

219155_at

phosphatidylinositol transfer

protein, cytoplasmic 1

227163_at

glutathione S-transferase

omega 2

209633_at

protein phosphatase 2,

regulatory subunit B″, alpha

219681_s_at

RAB11 family interacting

protein 1 (class I)

221860_at

heterogeneous nuclear

ribonucleoprotein L

243296_at

Nicotinamide

phosphoribosyltransferase

237133_at

—

1556000_s_at

BTB (POZ) domain containing 7

204681_s_at

Rap guanine nucleotide

exchange factor (GEF) 5

215726_s_at

cytochrome b5 type A

(microsomal)

210886_x_at

TP53 target 1 (non-protein

coding)

226597_at

receptor accessory protein 6

204995_at

cyclin-dependent kinase 5,

regulatory subunit 1 (p35)

236119_s_at

small proline-rich protein 2G

219228_at

zinc finger protein 331

234971_x_at

phospholipase C, delta 3

201127_s_at

ATP citrate lyase

226880_at

Nuclear casein kinase and

cyclin-dependent kinase

substrate 1

209383_at

DNA-damage-inducible

transcript 3

204168_at

microsomal glutathione S-

transferase 2

239670_at

WNK lysine deficient protein

kinase 2

208512_s_at

myeloid/lymphoid or mixed-

lineage leukemia (trithorax homolog,

Drosophila); translocate

213281_at

Jun proto-oncogene

218310_at

potassium channel

tetramerisation domain

containing 7//I RAB guanine

nucleotide exchan

205151_s_at

TLR4 interactor with leucine-rich

repeats

218217_at

serine carboxypeptidase 1

205055_at

integrin, alpha E (antigen

CD103, human mucosal

lymphocyte antigen 1; alpha

polypeptide

215009_s_at

THAP9 antisense RNA 1 (non-

protein coding)

227484_at

SLIT-ROBO Rho GTPase

activating protein 1

239769_at

Cadherin 11, type 2, OB-cadherin

230360_at

(osteoblast) gliomedin

227112_at

transmembrane and coiled-coil

domain family 1

201482_at

quiescin 06 sulfhydryl oxidase

1

210337_s_at

ATP citrate lyase

203911_at

RAP1 GTPase activating

protein

206683_at

zinc finger protein 165

202935_s_at

SRY (sex determining region

Y)-box 9

218951_s_at

phosphatidylinositol-specific

phospholipase C, X domain

containing 1

233488_at

ribonuclease, RNase A family, 7

202562_s_at

chromosome 14 open reading

frame 1

208745_at

ATP synthase, H+ transporting,

mitochondrial Fo complex,

subunit G

236078_at

KIAA1609

226226_at

transmembrane protein 45B

213854_at

synaptogyrin 1

243955_at

—

222111_at

family with sequence similarity

63, member B

1560296_at

—

240038_at

—

211372_s_at

interleukin 1 receptor, type II

202672_s_at

activating transcription factor 3

218717_s_at

leprecan-like 1

228366_at

—

230516_at

Mitochondrial assembly of

ribosomal large subunit 1

201920_at

solute carrier family 20

(phosphate transporter),

member 1

209632_at

protein phosphatase 2,

regulatory subunit B″, alpha

207367_at

ATPase, H+/K+ transporting,

nongastric, alpha polypeptide

1557256_a_at

—

200811_at

cold inducible RNA binding

protein

205201_at

GLI family zinc finger 3

227724_at

uncharacterized LOC0728190

205403_at

interleukin 1 receptor, type II

242827_x_at

—

228084_at

phospholipase A2, group XIIA

209365_s_at

extracellular matrix protein 1

243279_at

—

224946_s_at

coiled-coil domain containing

115

218708_at

NTF2-like export factor 1

1560531_at

late cornified envelope 1B

207761_s_at

methyltransferase like 7A

206011_at

caspase 1, apoptosis-related

cysteine peptidase

213703_at

long intergenic non-protein

coding RNA 342

224595_at

solute carrier family 44,

member 1

224613_s_at

DnaJ (Hsp40) homolog,

subfamily C, member 5

212504_at

DIP2 disco-interacting protein 2

homolog C (Drosophila)

213682_at

nucleoporin 50kDa

205247_at

notch 4

228235_at

uncharacterized protein

MGC16121

242873_at

—

205960_at

pyruvate dehydrogenase

kinase, isozyme 4

230494_at

solute carrier family 20

(phosphate transporter),

member 1

221260_s_at

cysteine-serine-rich nuclear

protein 2

224480_s_at

1-acylglycerol-3-phosphate 0-

acyltransferase 9

210180_s_at

transformer 2 beta homolog

(Drosophila)

204621_s_at

nuclear receptor subfamily 4,

group A, member 2

217863_at

protein inhibitor of activated

STAT, 1

236423_at

—

223421_at

cysteine/histidine-rich 1

220272_at

basonuclin 2

201791_s_at

7-dehydrocholesterol reductase

215574_at

—

224328_s_at

late cornified envelope 3D

211828_s_at

TRAF2 and NCK interacting

kinase

58367_s_at

zinc finger protein 419

218950_at

ArfGAP with RhoGAP domain,

ankyrin repeat and PH domain

3

1552703_s_at

caspase recruitment domain

family, member 16///caspase

1, apoptosis-related cysteine

219687_at

hedgehog acyltransferase

232127_at

chloride channel, voltage-sensitive 5

218377_s_at

RWD domain containing 2B

210335_at

Ras association (RaIGDS/AF-6)

domain family (N-terminal)

member 9

227927_at

—

227224_at

Ral GEF with PH domain and

SH3 binding motif 2

224778_s_at

TAO kinase 1

229566_at

WDNM1-like pseudogene

202734_at

thyroid hormone receptor

interactor 10

201851_at

SH3-domain GRB2-like 1

237337_at

—

37152_at

peroxisome proliferator-activated receptor

delta

209687_at

chemokine (C-X-C motif) ligand 12

203152_at

mitochondrial ribosomal protein

L40

201627_s_at

insulin induced gene 1

232593_at

neuralized homolog 3

(Drosophila) pseudogene

224769_at

TAO kinase 1

209702_at

fat mass and obesity associated

204546_at

KIAA0513

232224_at

mannan-binding lectin serine

peptidase 1 (C4/C2 activating

component of Ra-reactive fac

239930_at

UDP-N-acetyl-alpha-D-galactosamine:

polypeptide N-acetylgalactosaminyl-

transferase 2 (Gal

203178_at

glycine amidinotransferase (L-arginine:

glycine amidinotransferase)

235782_at

—

218181_s_at

mitogen-activated protein

kinase kinase kinase kinase 4

233520_s_at

cardiomyopathy associated 5

213456_at

sclerostin domain containing 1

219528_s_at

B-cell CLL/lymphoma 11B (zinc

finger protein)

224945_at

BTB (POZ) domain containing 7

214866_at

plasminogen activator,

urokinase receptor

209941_at

receptor (TNFRSF)-interacting

serine-threonine kinase 1

226029_at

yang-like 2 (van gogh,

Drosophila)

212596_s_at

HMG box domain containing 4

229873_at

potassium channel

tetramerisation domain

containing 21

226392_at

RAS p21 protein activator 2

226005_at

ubiquitin-conjugating enzyme

E2G 1

214445_at

elongation factor, RNA

polymerase II, 2

227680_at

zinc finger protein 326

227786_at

mediator complex subunit 30

222067_x_at

histone cluster 1, H2bd

1569106_s_at

SET domain containing 5

231785_at

neurotrophin 4

223937_at

forkhead box P1

1558685_a_at

uncharacterized protein

BC009467

211965_at

zinc finger protein 36, C3H

type-like 1

39549_at

neuronal PAS domain protein 2

203800_s_at

mitochondrial ribosomal protein

S14

1556321_a_at

—

212321_at

sphingosine-1-phosphate lyase

1

222154_s_at

spermatogenesis associated,

serine-rich 2-like

218774_at

decapping enzyme, scavenger

212268_at

serpin peptidase inhibitor, clade

B (ovalbumin), member 1

213134_x_at

BTG family, member 3

230669_at

RAS p21 protein activator 2

1559901_s_at

long intergenic non-protein

coding RNA 478

225298_at

paroxysmal nonkinesigenic

dyskinesia

242558_at

—

226043_at

G-protein signaling modulator 1

210236_at

protein tyrosine phosphatase,

receptor type, f polypeptide

(PTPRF), interacting protein

214066_x_at

natriuretic peptide receptor

B/guanylate cyclase B

(atrionatriuretic peptide receptor

B

240024_at

SEC14-like 2 (S. cerevisiae)

235462_at

Cytoplasmic polyadenylation

element binding protein 2

1554015_a_at

chromodomain helicase DNA

binding protein 2

235347_at

leucine-rich repeats and

calponin homology (CH)

domain containing 3

230847_at

Werner helicase interacting

protein 1

201427_s_at

selenoprotein P, plasma, 1

1557905_s_at

CD44 molecule (Indian blood

group)

219084_at

nuclear receptor binding SET

domain protein 1

206176_at

bone morphogenetic protein 6

219826_at

zinc finger protein 419

212356_at

KH and NYN domain containing

218909_at

ribosomal protein S6 kinase,

52kDa, polypeptide 1

230555_s_at

Mediator complex subunit 30

212687_at

LIM and senescent cell antigen-

like domains 1

203098_at

chromodomain protein, Y-like

229054_at

zinc finger protein 36, C3H

type-like 1

236039_at

LY6/PLAUR domain containing

5

209661_at

kinesin family member C3

209560_s_at

delta-like 1 homolog

(Drosophila)

225812_at

chromosome 6 open reading

frame 225

227829_at

glycosyltransferase-like 1B

238623_at

—

229415_at

cytochrome c, somatic

209222_s_at

oxysterol binding protein-like 2

1555809_at

cysteine-rich secretory protein

LCCL domain containing 2

204567_s_at

ATP-binding cassette, sub-family

G (WHITE), member 1

232277_at

solute carrier family 28 (sodium-

coupled nucleoside

transporter), member 3

237197_at

—

225209_s_at

ubiquitin-conjugating enzyme

E2, J2

231916_at

nitric oxide synthase 1

(neuronal)

212279_at

transmembrane protein 97

204862_s_at

NME/NM23 nucleoside

diphosphate kinase 3

230483_at

—

212856_at

GRAM domain containing 4

224650_at

mal, T-cell differentiation protein

2 (gene/pseudogene)

202963_at

regulatory factor X, 5

(influences HLA class II

expression)

225320_at

mitochondrial calcium uniporter

236274_at

eukaryotic translation initiation

factor 3, subunit B

209780_at

putative homeodomain

transcription factor 2

potassium channel

218823_s_at

tetramerisation domain

containing 9

227787_s_at

mediator complex subunit 30

230296_at

chromosome 16 open reading

frame 52

222892_s_at

transmembrane protein 40

210610_at

carcinoembryonic antigen-related

cell adhesion molecule1 (biliary

glycoprotein)

230031_at

heat shock 70kDa protein 5

(glucose-regulated protein,

78kDa)

238477_at

kinesin family member 1C

209409_at

growth factor receptor-bound

protein 10

217995_at

sulfide quinone reductase-like

(yeast)

226873_at

family with sequence similarity

63, member B

1553722_s_at

ring finger protein 152

204710_s_at

WD repeat domain,

phosphoinositide interacting 2

212653_s_at

EH domain binding protein 1

203979_at

cytochrome P450, family 27,

subfamily A, polypeptide 1

244350_at

myosin X

223233_s_at

cingulin

1555967_at

—

214355_x_at

CTAGE family, member 15,

pseudogene///CTAGE family,

member 4///CTAGE family,

member

214469_at

histone cluster 1, H2ab///

histone cluster 1, H2ae

212472_at

microtubule associated

monoxygenase, calponin and

LIM domain containing 2

228115_at

family with sequence similarity

59, member A

228964_at

PR domain containing 1, with

ZNF domain

230027_s_at

mitochondrial ribosomal protein

L43

207318_s_at

cyclin-dependent kinase 13

221689_s_at

phosphatidylinositol glycan

anchor biosynthesis, class P

219270_at

ChaC, cation transport regulator

homolog 1 (E. coli)

225299_at

myosin VB

239770_at

extended synaptotagmin-like

protein 3

226399_at

DnaJ (Hsp40) homolog,

subfamily B, member 14

226656_at

cartilage associated protein

228852_at

endosulfine alpha

206239_s_at

serine peptidase inhibitor, Kazal

type 1

210993_s_at

SMAD family member 1

238462_at

ubiquitin associated and SH3

domain containing B

211962_s_at

zinc finger protein 36, C3H

type-like 1

224666_at

non-SMC element 1 homolog

(S. cerevisiae)

239028_at

LY6/PLAUR domain containing

6

213577_at

squalene epoxidase

202011_at

tight junction protein 1 (zona

occludens 1)

212254_s_at

dystonin///dystonin-like

221701_s_at

stimulated by retinoic acid gene

6 homolog (mouse)

239576_at

microtubule associated tumor

suppressor 1

234418_x_at

CD44 molecule (Indian blood

group)

227985_at

uncharacterized

LOC100506098

213462_at

neuronal PAS domain protein 2

224975_at

nuclear factor I/A

225990_at

Boc homolog (mouse)

240616_at

—

219911_s_at

solute carrier organic anion

transporter family, member 4A1

224970_at

nuclear factor I/A

214623_at

F-box and WD repeat domain

containing 4 pseudogene 1

239478_x_at

chromosome 14 open reading

frame 118

226909_at

zinc finger protein 518B

208670_s_at

EP300 interacting inhibitor of

differentiation 1

206192_at

corneodesmosin

222173_s_at

TBC1 domain family, member 2

228450_at

pleckstrin homology domain

containing, family A member 7

1558097_at

proline rich 14-like

219373_at

dolichyl-phosphate

mannosyltransferase

polypeptide 3

230388_s_at

KANSL1 antisense RNA 1 (non-

protein coding)

207098_s_at

mitofusin 1

223484_at

chromosome 15 open reading

frame 48

244804_at

sequestosome 1

229679_at

chromosome 12 open reading

frame 76

225826_at

methylmalonic aciduria

(cobalamin deficiency) cbIB

type

213352_at

transmembrane and coiled-coil

domain family 1

211883_x_at

carcinoembryonic antigen-related

cell adhesion molecule 1 (biliary

glycoprotein)

210387_at

histone cluster 1, H2bc///

histone cluster 1, H2be///

histone cluster 1, H2bf///his

210916_s_at

CD44 molecule (Indian blood

group)

221432_s_at

solute carrier family 25

(mitochondrial iron transporter),

member 28

218487_at

aminolevulinate dehydratase

223264_at

mesoderm development

candidate 1

206356_s_at

guanine nucleotide binding

protein (G protein), alpha

activating activity polypeptide,

218097_s_at

CUE domain containing 2

228001_at

transmembrane protein 50B

212441_at

K1AA0232

201854_s_at

ATM interactor

121_at

paired box 8

222143_s_at

myotubularin related protein 14

1558002_at

Serine/threonine kinase

receptor associated protein

226040_at

—

226141_at

coiled-coil domain containing

149

1556567_at

nucleosome assembly protein

1-like 4

226263_at

small nuclear ribonucleoprotein

48kDa (U11/U12)

212074_at

Sad1 and UNC84 domain

containing 1

227387_at

Non-SMC element 4 homolog A

(S. cerevisiae)

232795_at

—

203936_s_at

matrix metallopeptidase 9

(gelatinase B, 92kDa

gelatinase, 92kDa type IV

collagenase)

225033_at

ST3 beta-galactoside alpha-2,3-

sialyltransferase 1

209109_s_at

tetraspanin 6

213351_s_at

transmembrane and coiled-coil

domain family 1

203047_at

serine/threonine kinase 10

220721_at

zinc finger protein 614

1556127_at

DIP2 disco-interacting protein 2

homolog A (Drosophila)

215016_x_at

dystonin///dystonin-like

206576_s_at

carcinoembryonic antigen-related

cell adhesion molecule

1 (biliary glycoprotein)

240674_at

jumonji, AT rich interactive

domain 2

225646_at

cathepsin C

1554010_at

N-deacetylase/N-sulfotransferase

(heparan glucosaminyl) 1

204100_at

thyroid hormone receptor, alpha

221840_at

protein tyrosine phosphatase,

receptor type, E

209078_s_at

thioredoxin 2

218530_at

formin homology 2 domain

containing 1

235434_at

—

230063_at

zinc finger protein 264

40420_at

serine/threonine kinase 10

221027_s_at

phospholipase A2, group XIIA

244202_at

—

212108_at

Fas associated factor family

member 2

204294_at

aminomethyltransferase

225503_at

dehydrogenase/reductase

(SDR family) X-linked

212810_s_at

solute carrier family 1

(glutamate/neutral amino acid

transporter), member 4

214814_at

YTH domain containing 1

228468_at

microtubule associated

serine/threonine kinase-like

209108_at

tetraspanin 6

220444_at

zinc finger protein 557

206172_at

interleukin 13 receptor, alpha 2

225002_s_at

sulfatase modifying factor 2

212205_at

H2A histone family, member V

228851_s_at

endosulfine alpha

209048_s_at

zinc finger, MYND-type

containing 8

211846_s_at

poliovirus receptor-related 1

(herpesvirus entry mediator C)

238909_at

S100 calcium binding protein

A10

205503_at

protein tyrosine phosphatase,

non-receptor type 14

243829_at

v-raf murine sarcoma viral

oncogene homolog B1

244379_at

—

223251_s_at

ankyrin repeat domain 10

202633_at

topoisomerase (DNA) II binding

protein 1

214502_at

histone cluster 1, H2bj

221773_at

ELK3, ETS-domain protein

(SRF accessory protein 2)

41858_at

post-GPI attachment to proteins

2

212850_s_at

low density lipoprotein receptor-

related protein 4

223408_s_at

—

214472_at

histone cluster 1, H2ad///

histone cluster 1, H3a///

histone cluster 1, H3b///histo

225647_s_at

cathepsin C

1559977_a_at

solute carrier family 25,

member 34

211347_at

CDC14

homolog B (S. cerevisiae)

1558208_at

—

227570_at

transmembrane protein 86A

227492_at

occludin pseudogene///

occludin

1558778_s_at

MKL/myocardin-like 2

31637_s_at

nuclear receptor subfamily 1,

group D, member 1///thyroid

hormone receptor, alpha

229190_at

uncharacterized

LOC100507376

236188_s_at

Nucleosome assembly protein

1-like 4

212503_s_at

DIP2 disco-interacting protein 2

homolog C (Drosophila)

204760_s_at

nuclear receptor subfamily 1,

group D, member 1///thyroid

hormone receptor, alpha

212099_at

ras homolog family member B

214873_at

low density lipoprotein receptor-

related protein 5-like

228181_at

solute carrier family 30 (zinc

transporter), member 1

212763_at

calmodulin regulated spectrin-

associated protein family,

member 2

226285_at

cell cycle associated protein 1

213567_at

karyopherin alpha 4 (importin

alpha 3)

203927_at

nuclear factor of kappa light

polypeptide gene enhancer in

B-cells inhibitor, epsilon

208523_x_at

histone cluster 1, H2bc///

histone cluster 1, H2be///

histone cluster 1, H2bf///his

219389_at

sushi domain containing 4

202329_at

c-src tyrosine kinase

238523_at

kelch-like 36 (Drosophila)

1565016_at

protein arginine

methyltransferase 1

226409_at

TBC1 domain family, member

20

229926_at

microRNA 3682

208527_x_at

histone cluster 1, H2bc///

histone cluster 1, H2be///

histone cluster 1, H2bf///his

223598_at

RAD23 homolog B (S.

cerevisiae)

243797_at

serine/threonine kinase 17b

203317_at

pleckstrin and Sec7 domain

containing 4

230965_at

ubiquitin specific peptidase 2

208490_x_at

histone cluster 1, H2bc///

histone cluster 1, H2be///

histone cluster 1, H2bf///his

235514_at

aspartic peptidase, retroviral-

like 1

209098_s_at

jagged 1

1554229_at

CREB3 regulatory factor

209398_at

histone cluster 1, H1c

202629_at

amyloid beta precursor protein

(cytoplasmic tail) binding

protein 2

203428_s_at

ASF1 anti-silencing function 1

homolog A (S. cerevisiae)

238005_s_at

SIN3 transcription regulator

homolog A (yeast)

214455_at

histone cluster 1, H2bc///

histone cluster 1, H2be///

histone cluster 1, H2bf///his

214073_at

cortactin

203140_at

B-cell CLL/lymphoma 6

232150_at

—

208546_x_at

histone cluster 1, H2bh

243446_at

ajuba LIM protein

236207_at

sperm specific antigen 2

212016_s_at

polypyrimidine tract binding

protein 1

232311_at

Beta-2-microglobulin

219711_at

zinc finger protein 586

208579_x_at

H2B histone family, member S

(pseudogene)///histone cluster

1, H2bk

239493_at

ribosomal protein L7

214074_s_at

cortactin

228091_at

syntaxin 17

234331_s_at

family with sequence similarity

84, member A

212372_at

myosin, heavy chain 10, non-muscle

 Or, from genes for each of the pharmacodynamic biomarkers from the list further consisting of:

MMP2

ESR1

FOS

PCLG2

MAPK6

JUN

COND1

PPAR1

MAPK1

MAPK7

CEBPA

MAPK3

PCLG1

MAPK4

MAPK12

AKT2

CASP3

FOS

HSP90AB1

JUN

BAG3

CCND1

HASP90AA1

HSP90B1

AKT1

ARG2

CCNA1

CCND2

CCNE2

TNF

BDNF

CCNA2

CCNE1

CTF1

BRAF

ARG2

CCND2

TNF

PPP3R1

CALM3

BDNF

CCNE1

PPP3CA

PPP3R2

CAMK1

CCNA1

CCNE2

PPP3CB

CALM1

CAMK1D

CCNA2

CTF1

PPP3CC

CALM2

CAMK1G

BDNF

CCNE1

PPP3CC

ORAI3

TNF

CCNA1

PPP3CB

CAMK2D

CCND2

CALM3

PPP3CA

CACNA2D4

CHRNB3

HDAC10

PPP3CB

CACNB1

CHRNB4

HDAC11

PPP3CC

CACNB2

CHRND

HDAC2

PPP3R1

CACNB3

CHRNE

HDAC3

PPP3R2

CACNB4

CHRNG

HDAC4

ATP2C1

CACNG1

GRIA1

HDAC5

CACNA1A

CHRFAM7A

GRIA2

HDAC6

CACNA1B

CHRNA1

GRIA3

HDAC7

CACNA1C

CHRNA10

GRIA4

HDAC8

CACNA1D

CHRNA2

GRIK1

HDAC9

CACNA1F

CHRNA3

GRIN1

HTR3A

CACNA1H

CHRNAS

GRIN2B

SLC8A1

CACNA2I

CHRNA6

GRIN2C

TNNC1

CACNA1G

CHRNA4

GRIN2A

RYR1

CACNA1S

CHRNA7

GRIN2D

CACNA2D1

CHRNA9

GRIN3A

CACNA2D2

CHRNB1

GRIN3B

CACNA2D3

CHRNB2

HDAC1

CACNA2D1

CHRNA9

GRIN3A

CACNA2D2

CHRNB1

GRIN3B

CACNA2D3

CHRNB2

HDACC1

MAP15

AKT1

MOS3

HSP90B1

CASP3

AKT2

HSP90AA1

Hsp84-2

HSPA8

AKT3

HSP90AB1

Hsp84-3

BAG3

CEBPA

MAPK3

MAPK1

MAPK7

CA9

CALR

CAMK2A

CAMK4

ORAI3

TRPC3

TRPC7

CAMK2B

NOS2

STIM1

TRPC4

BRAF

CAMK2D

ORAI2

STIM2

TRPC5

CA9

CAMK2G

ORAI2

TRPC1

TRPC6

CALR

CAMK1

ORAI2

BRAF

CAMK2G

STIM2

CALR

 Or, from genes for each of the pharmacodynamic biomarkers from the list further consisting of:

ABCC5

CYHR1

HIST3H2A

POU2F3

ATP6V1B1

DEPTOR

HOXB13

RAMP1

ATXN3

DNAL4

ING4

SEMA3G

BCAS1

EIF4A2

OVGP1

SEPP1

BCL2L11

EPHX2

PCMTD1

SIDT2

CALCOCO1

ERBB3

PCMTD2

AREG

CAPN13

HIST1H2AC

PDIA4

BTG3

CRBN

HIST1H2BD

PLEKHG4

CEBPG

CORO1C

IFRD1

PFKP

DLEU2

IMPAD1

PNPT1

DPH3

KLK6

PSMC4

EIF5

KPNA4

RPS6KA3

ENO2

LRP8

S100A2

HN1

MALL

SERPINB5

HSP90AA1

MTHFD1L

SERPINB8

HSPA4L

PADI1

SLC7A1

SRXN1

TIPIN;

 and

d) identifying, using the calculated signature scores and quantitated responses, each of the pharmacodynamics biomarkers of each of the signature pathways by at least 3 or more genes listed in 1c).

2. The method of claim 1 , wherein the pharmacodynamic biomarkers of each of the signature pathways further include at least 3 or more genes for which pharmacodynamics biomarkers are from the list consisting of:

ABCC5

CYHR1

HIST3H2A

POU2F3

ATP6V1B1

DEPTOR

HOXB13

RAMP1

ATXN3

DNAL4

ING4

SEMA3G

BCAS1

EIF4A2

OVGP1

SEPP1

BCL2L11

EPHX2

PCMTD1

SIDT2

CALC0001

ERBB3

PCMTD2

AREG

CAPN13

HIST1H2AC

PDIA4

BTG3

CRBN

HIST1H2BD

PLEKHG4

CEBPG

CORO1C

IFRD1

PFKP

DLEU2

IMPAD1

PNPT1

DPH3

KLK6

PSMC4

EIF5

KPNA4

RPS6KA3

EN02

LRP8

S100A2

HN1

MALL

SERPINB5

HSP9OAA1

MTHFD1L

SERPINB8

HSPA4L

PADI1

SLC7A1

SRXN1

TIPIN.

3. The method of claim 2 , wherein at least one of the signature pathways is RAS.

4. The method of claim 3 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for RAS is inhibited in response to exposure to CTO.

5. The method of claim 2 , wherein at least one of the signature pathways is GFS.

6. The method of claim 5 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for GFS is inhibited in response to exposure to CTO.

7. The method of claim 1 , wherein at least one of the signature pathways is MEKi.

8. The method of claim 5 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for MEKi is inhibited in response to exposure to CTO.

9. The method of claim 1 , wherein at least one of the signature pathways is HDAC.

10. The method of claim 9 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for HDAC is inhibited in response to exposure to CTO.

11. The method of claim 1 , wherein at least one of the signature pathways is NOTCH.

12. The method of claim 11 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for NOTCH is inhibited in response to exposure to CTO.

13. The method of claim 1 , wherein at least one of the signature pathways is WNTβ-catenin.

14. The method of claim 13 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for WNTβ-catenin is inhibited in response to exposure to CTO.

15. The method of claim 1 , wherein at least one of the signature pathways is HSP90.

16. The method of claim 15 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for HSP90 is inhibited in response to exposure to CTO.

17. The method of claim 1 , wherein at least one of the signature pathways is EGFR.

18. The method of claim 17 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for EGFR is inhibited in response to exposure to CTO.

19. The method of claim 1 , wherein at least one of the signature pathways is P53.

20. The method of claim 19 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for P53 is induced in response to exposure to CTO.

21. The method of claim 1 , wherein at least one of the signature pathways is EGR1.

22. The method of claim 21 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for EGR1 is stimulated in response to exposure to CTO.

23. The method of claim 1 , wherein at least one of the signature is CEACAMI.

24. The method of claim 23 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for CEACAMI is stimulated in response to exposure to CTO.

25. The method of claim 1 , wherein at least one of the signature pathways is TGFβ.

26. The method of claim 25 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for TGFβ is stimulated in response to exposure to CTO.

27. The method of claim 1 , wherein at least one of the signature pathways is Dystonin.

28. The method of claim 27 , wherein the signature score of the pharmacodynamic biomarkers of the signature pathways for Dystonin is stimulated in response to exposure to CTO.