Supplementary Table S2 List of discriminating genes (177 probe sets) between MSI and MSS cancers

Probe ID

Fold change (MSI/MSS)

FDR P value

Gene Symbol

GenBank

Gene Name

223694_at

12.84

1.75E-12

TRIM7

AF220032

tripartite motif-containing 7

215505_s_at

10.45

5.24E-21

STRN3

AF243424

striatin, calmodulin binding protein 3

223447_at

9.41

0.0000157

REG4

AY007243

regenerating islet-derived family, member 4

1554436_a_at

9.174

0.0000126

REG4

AY126671

regenerating islet-derived family, member 4

201123_s_at

8.501

1.73E-11

EIF5A

NM_001970

eukaryotic translation initiation factor 5A

214385_s_at

8.137

0.00167

AI521646

to66a06.x1 NCI_CGAP_Gas4 Homo sapiens cDNA clone IMAGE:2183218 3' similar to TR:Q13792 Q13792 APOMUCIN ;, mRNA sequence.

226913_s_at

6.892

0.000415

BF527050

602039960F2 NCI_CGAP_Brn67 Homo sapiens cDNA clone IMAGE:4177598 5', mRNA sequence.

206108_s_at

6.789

1.73E-11

SFRS6

NM_006275

splicing factor, arginine/serine-rich 6

204014_at

6.549

0.00000133

DUSP4

NM_001394

dual specificity phosphatase 4

203444_s_at

6.474

5.35E-13

MTA1L1

NM_004739

metastasis-associated 1-like 1

214303_x_at

5.946

0.00287

MUC5AC

AW192795

mucin 5, subtypes A and C, tracheobronchial/gastric

1569062_s_at

5.897

3.19E-08

IQGAP3

BC033549

IQ motif containing GTPase activating protein 3

213380_x_at

5.677

0.000000266

MSTP9

AA911235

macrophage stimulating, pseudogene 9

205614_x_at

5.364

1.98E-08

MST1

NM_020998

macrophage stimulating 1 (hepatocyte growth factor-like)

210145_at

5.185

0.0000507

PLA2G4A

M68874

phospholipase A2, group IVA (cytosolic, calcium-dependent)

205501_at

5.053

0.00000462

AI143879

Homo sapiens cDNA FLJ25677 fis, clone TST04054

228969_at

4.96

1.26E-08

AGR2

AI922323

anterior gradient 2 homolog (Xenopuslaevis)

231768_at

4.933

0.000000264

USF1

X55666

upstream transcription factor 1

203349_s_at

4.759

0.000000249

ETV5

NM_004454

ets variant gene 5 (ets-related molecule)

226034_at

4.749

0.00000345

na

BE222344

Homo sapiens, clone IMAGE:3881549, mRNA

205278_at

4.745

0.000426

GAD1

NM_000817

glutamate decarboxylase 1 (brain, 67kDa)

204073_s_at

4.701

0.000000207

C11orf9

NM_013279

chromosome 11 open reading frame 9

223642_at

4.662

0.00163

ZIC2

AF193855

Zic family member 2 (odd-paired homolog, Drosophila)

212859_x_at

4.624

5.05E-09

MT2A

BF217861

metallothionein 2A

211140_s_at

4.615

0.00000024

CASP2

AF314174

caspase 2, apoptosis-related cysteine protease (neural precursor cell expressed, developmentally down-regulated 2)

239694_at

4.569

6.69E-08

TRIM7

AA527412

tripartite motif-containing 7

204653_at

4.446

0.000000108

TFAP2A

BF343007

transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)

205081_at

4.375

0.00000217

CRIP1

NM_001311

cysteine-rich protein 1 (intestinal)

209812_x_at

4.372

0.0000102

CASP2

U13021

caspase 2, apoptosis-related cysteine protease (neural precursor cell expressed, developmentally down-regulated 2)

228708_at

4.329

0.000000183

RAB27B

BF438386

RAB27B, member RAS oncogene family

202072_at

4.304

7.03E-12

HNRPL

NM_001533

heterogeneous nuclear ribonucleoprotein L

204415_at

4.3

0.00000804

G1P3

NM_022873

interferon, alpha-inducible protein (clone IFI-6-16)

201122_x_at

4.275

1.45E-10

EIF5A

BC000751

eukaryotic translation initiation factor 5A

209949_at

4.136

0.000018

NCF2

BC001606

neutrophilcytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2)

216320_x_at

4.126

0.00000868

MST1; MSP; HGFL; NF15S2; D3F15S2; DNF15S2

U37055

Human hepatocyte growth factor-like protein gene, complete cds.

235901_at

4.111

0.0000203

BE671060

Homo sapiens transcribed sequences

216834_at

4.047

0.000583

RGS1

S59049

regulator of G-protein signalling 1

230964_at

0.25

0.00137

N66307

yz37h06.s1 Morton Fetal Cochlea Homo sapiens cDNA clone IMAGE:285275 3', mRNA sequence.

244508_at

0.249

0.00000252

N39126

Homo sapiens transcribed sequences

239884_at

0.248

0.000145

CADPS

BE467579

Ca2+-dependent activator protein for secretion

204364_s_at

0.247

0.00000819

FLJ13110

BE535746

hypothetical protein FLJ13110

206755_at

0.247

0.0000152

CYP2B6

NM_000767

cytochrome P450, family 2, subfamily B, polypeptide 6

1553333_at

0.245

0.000015

FLJ38716

AW301313

hypothetical protein FLJ38716

1555867_at

0.245

0.000262

GNG4

AK022067

guanine nucleotide binding protein (G protein), gamma 4

214912_at

0.245

0.0000161

AW173003

Homo sapiens cDNA FLJ12005 fis, clone HEMBB1001565.

220065_at

0.245

0.0000718

TNMD

NM_152367

tenomodulin protein

238381_x_at

0.245

0.00000957

BM666010

xs75b04.x1 NCI_CGAP_Lu26 Homo sapiens cDNA clone IMAGE:2775439 3', mRNA sequence.

239614_x_at

0.245

0.00000365

NM_022144

Homo sapiens transcribed sequences

205184_at

0.244

0.0000102

GNG4

AI392908

guanine nucleotide binding protein (G protein), gamma 4

230352_at

0.244

0.000000573

PRPS2

NM_004485

phosphoribosyl pyrophosphate synthetase 2

205471_s_at

0.243

0.00000118

DACH

AW772082

dachshund homolog (Drosophila)

243172_at

0.242

0.000104

na

AI079944

Homo sapiens cDNA FLJ36394 fis, clone THYMU2009104

1554781_at

0.24

0.000118

MGC32805

S64699

hypothetical protein MGC32805

232707_at

0.24

0.00186

LOC91464

N39099

Homo sapiens cDNA: FLJ21528 fis, clone COL05977

234702_x_at

0.24

0.000282

CFTR

BC029465

cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)

243623_at

0.24

0.0000236

SLC1A7

AK025181

solute carrier family 1 (glutamate transporter), member 7

1555086_at

0.239

0.00000682

STAT5B

BM352108

signal transducer and activator of transcription 5B

1557810_at

0.239

4.96E-09

AL359055

Homo sapiens clone HEA5 Cri-du-chat critical region mRNA

1566764_at

0.239

7.08E-08

BC020868

Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2344436

222771_s_at

0.238

0.00244

MYEF2

BF224052

myelin expression factor 2

1569238_a_at

0.237

0.00000213

BF062804

Homo sapiens cDNA clone IMAGE:4770316, partial cds

237146_at

0.237

0.00000026

BE348304

Homo sapiens transcribed sequences

237554_at

0.237

0.00000108

BC033052

Homo sapiens transcribed sequences

202410_x_at

0.236

0.00331

IGF2

NM_000612

insulin-like growth factor 2 (somatomedin A)

219658_at

0.236

0.00000149

FLJ12598

AA778747

hypothetical protein FLJ12598

241941_at

0.236

0.00000143

NM_024754

Homo sapiens cDNA FLJ31511 fis, clone NT2RI1000035.

206696_at

0.233

0.0000429

GPR143

NM_000273

G protein-coupled receptor 143

230043_at

0.232

0.0000168

na

BE670584

Homo sapiens transcribed sequences

231341_at

0.232

0.000365

AI168678

Homo sapiens transcribed sequences

228262_at

0.231

0.00207

FLJ14503

AW237462

hypothetical protein FLJ14503

242736_at

0.231

0.00000223

AI377221

Homo sapiens transcribed sequences

216775_at

0.23

0.00000754

KIAA1350

AL037450

KIAA1350 protein

236223_s_at

0.23

5.9E-09

RIT1

AK025301

Ras-like without CAAX 1

1568604_a_at

0.229

0.000972

CADPS

AV655991

Ca2+-dependent activator protein for secretion

231693_at

0.229

0.000158

FABP1

AI912173

fatty acid binding protein 1, liver

226085_at

0.228

1.03E-10

CBX5

AA181060

Homo sapiens, clone IMAGE:5288883, mRNA

231426_at

0.228

0.000119

MGC34760

AW271796

hypothetical protein MGC34760

243233_at

0.228

0.0000025

AI701943

tq09b09.x1 NCI_CGAP_Ut3 Homo sapiens cDNA clone IMAGE:2208281 3', mRNA sequence.

226400_at

0.227

1.75E-12

CDC42

N92917

cell division cycle 42 (GTP binding protein, 25kDa)

213953_at

0.223

0.000677

KRT20

AI732381

keratin 20

1552691_at

0.222

0.000456

ARLTS1

AF118887

ADP-ribosylation factor-like tumor suppressor protein 1

218806_s_at

0.222

0.000283

VAV3

BF223464

vav 3 oncogene

229841_at

0.222

1.34E-10

EIF2C2

NM_138450

eukaryotic translation initiation factor 2C, 2

1565811_at

0.221

0.0000002

BC033945

Homo sapiens, clone IMAGE:5278245, mRNA

213788_s_at

0.221

2.27E-10

na

AI701156

Homo sapiens clone 23718 mRNA sequence

205472_s_at

0.22

0.0000223

DACH

NM_004392

dachshund homolog (Drosophila)

1556800_a_at

0.218

0.00000152

BC041397

Homo sapiens cDNA clone IMAGE:5277448, partial cds

236139_at

0.217

0.000000254

BE671815

Homo sapiens transcribed sequences

1568603_at

0.216

0.000815

CADPS

AI912173

Ca2+-dependent activator protein for secretion

203628_at

0.216

2.73E-10

AI820802

yl77f04.s1Soares infant brain 1NIB Homo sapiens cDNA clone IMAGE:44149 3', mRNA sequence.

232628_at

0.216

0.00000288

H05812

Homo sapiens cDNA FLJ13464 fis, clone PLACE1003478.

237943_at

0.216

0.000000558

KIAA0779

AI740629

KIAA0779 protein

44790_s_at

0.214

0.0000182

4838516_RC

Cluster Incl. AI129310:qc48a05.x1 Homo sapiens cDNA, 3 end /clone=IMAGE-1712816 /clone_end=3' /gb=AI129310 /gi=3597824 /ug=Hs.234923 /len=811

236524_at

0.212

1.92E-09

AA737437

Homo sapiens cDNA FLJ37319 fis, clone BRAMY2018027.

211207_s_at

0.211

0.000172

FACL6

AF129166

fatty-acid-Coenzyme A ligase, long-chain 6

230002_at

0.211

2.38E-12

MCLC

AV693734

Mid-1-related chloride channel 1

239449_at

0.211

1.33E-08

AA406603

Homo sapiens transcribed sequence with weak� similarity to protein ref:NP_060265.1 (H.sapiens)� hypothetical protein FLJ20378 [Homo sapiens]

1559156_at

0.21

0.00000178

NM_022097

Homo sapiens, clone IMAGE:5266106, mRNA

206149_at

0.21

0.00122

LOC63928

AV687517

hepatocellular carcinoma antigen gene 520

228498_at

0.21

0.000000597

B4GALT1

BC036508

UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1

222787_s_at

0.208

9.38E-14

FLJ11273

AV705186

hypothetical protein FLJ11273

204712_at

0.207

0.0000542

WIF1

NM_007191

WNT inhibitory factor 1

216255_s_at

0.206

0.0000879

GRM8; GLUR8; mGlu8; GPRC1H; MGLUR8

AC000099

Homo sapiens chromosome 7 map 7q31.3 cosmid g0771a003, complete sequence.

233877_at

0.206

1.45E-09

AK000777

Homo sapiens cDNA FLJ20770 fis, clone COL06509

205097_at

0.203

4.53E-08

SLC26A2

AI304862

solute carrier family 26 (sulfate transporter), member 2

239131_at

0.203

1.27E-10

AI025519

Homo sapiens transcribed sequences

217617_at

0.202

0.0000192

AW451711

Homo sapiens transcribed sequence with weak� similarity to protein ref:NP_060312.1 (H.sapiens)� hypothetical protein FLJ20489 [Homo sapiens]

230921_s_at

0.2

5.05E-09

DKFZP564J157

BE467612

DKFZp564J157 protein

1555882_at

0.199

0.000636

AJ271379

Homo sapiens cDNA FLJ45577 fis, clone BRTHA3011265, highly� similar to Spindlin

236975_at

0.197

0.00000416

BF515552

Homo sapiens transcribed sequences

212768_s_at

0.196

0.00428

bA209J19.1

AL390736

isoform 1 match: proteins: Sw:Q07081 Tr:O95362 Tr:Q9Z2Y4 Tr:O95897 Tr:O70624 Sw:Q99972 Sw:Q99784 Sw:Q62609 Tr:Q9TV76 Tr:Q9I9K5 Sw:P01813 Tr:Q9IAK4 Tr:O35429; Human DNA sequence from clone RP11-209J19 on chromosome 13 Contains ESTs, STSs and GSSs. Contains the gene for the GW112 protein with two isoforms (GW112 and KIAA4294), complete sequence.

233317_at

0.195

0.000000903

AK025016

Homo sapiens cDNA: FLJ21363 fis, clone COL02986

1563331_at

0.194

0.000000254

BU561086

Homo sapiens clone FBD10 Cri-du-chat region mRNA

222484_s_at

0.192

0.00103

CXCL14

N66045

chemokine (C-X-C motif) ligand 14

243341_at

0.192

7.72E-08

AF144103

Homo sapiens transcribed sequences

228307_at

0.191

1.65E-08

EMILIN5; Emilin3; C20orf130; dJ620E11.4; DKFZp434A2410

AL137580

Homo sapiens mRNA; cDNA DKFZp686P07216 (from clone DKFZp686P07216)

219727_at

0.19

0.000937

DUOX2

NM_014080

dual oxidase 2

231667_at

0.189

0.00000195

SLC39A5

AW614558

solute carrier family 39 (metal ion transporter), member 5

233458_at

0.189

3.85E-10

RPC5

AB040885

RNA polymerase III 80 kDa subunit RPC5

210282_at

0.184

1.11E-10

ZNF198

BE326919

zinc finger protein 198

230333_at

0.184

4.5E-10

SAT

AL136621

spermidine/spermine N1-acetyltransferase

206239_s_at

0.182

0.00000754

SPINK1

AA393940

serine protease inhibitor, Kazal type 1

213757_at

0.182

0.00000101

EIF5A

NM_003122

eukaryotic translation initiation factor 5A

242277_at

0.182

4.04E-10

C6orf56

AW880875

chromosome 6 open reading frame 56

205405_at

0.181

1.01E-08

SEMA5A

NM_003966

sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A

222313_at

0.18

0.00000236

AW972359

Homo sapiens transcribed sequences

229704_at

0.18

2.13E-12

APRIN

BF111072

androgen-induced proliferation inhibitor

230291_s_at

0.178

0.000000467

NFIB

T90642

nuclear factor I/B

238611_at

0.177

0.00000103

HNRPM

AI906424

heterogeneous nuclear ribonucleoprotein M

233604_at

0.174

0.00000217

AI650260

Homo sapiens cDNA: FLJ22763 fis, clone KAIA0963

204607_at

0.173

0.000418

HMGCS2

N64867

3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)

239589_at

0.173

4.76E-09

NM_005518

Homo sapiens transcribed sequences

205549_at

0.171

0.000011

PCP4

AW663083

Purkinje cell protein 4

236617_at

0.171

1.59E-08

AA053853

Homo sapiens, clone IMAGE:5285945, mRNA

244187_at

0.171

0.000000199

UNQ8193

NM_006198

AAIR8193

240758_at

0.169

1.24E-08

AA706753

Homo sapiens transcribed sequences

238673_at

0.165

3.09E-08

AV724325

Homo sapiens transcribed sequences

1556054_at

0.164

4.54E-08

TBC1D8

AI034387

TBC1 domain family, member 8 (with GRAM domain)

230085_at

0.161

8.21E-10

AW263542

Homo sapiens transcribed sequences

242967_at

0.161

0.00000388

AI264125

qk03a05.x1 NCI_CGAP_Kid3 Homo sapiens cDNA clone IMAGE:1867856 3', mRNA sequence.

233404_at

0.159

0.000000629

na

AU158588

Homo sapiens cDNA FLJ13756 fis, clone PLACE3000365.

226907_at

0.158

0.000125

PPP1R14C

N32557

protein phosphatase 1, regulatory (inhibitor) subunit 14C

244023_at

0.158

0.000000113

SYK

AW467357

spleen tyrosine kinase

218002_s_at

0.156

0.000573

CXCL14

NM_004887

chemokine (C-X-C motif) ligand 14

213789_at

0.154

5.21E-09

EBP

N58493

emopamil binding protein (sterol isomerase)

227735_s_at

0.154

0.00000585

AA553959

Homo sapiens clone DNA92219 RLLV1833 (UNQ1833) mRNA, complete cds

206286_s_at

0.153

0.0000424

TDGF1

W26593

teratocarcinoma-derived growth factor 1

213048_s_at

0.153

5.2E-11

NM_003212

33g5 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA, mRNA sequence.

222257_s_at

0.15

0.000000216

ACE2

AK026461

angiotensin I converting enzyme (peptidyl-dipeptidase A) 2

213369_at

0.149

0.000183

KIAA1775

AI825832

MT-protocadherin

219962_at

0.149

4.54E-08

ACE2

NM_021804

angiotensin I converting enzyme (peptidyl-dipeptidase A) 2

205892_s_at

0.146

0.0000234

FABP1

NM_001443

fatty acid binding protein 1, liver

230958_s_at

0.143

2.27E-08

BE670797

Homo sapiens mRNA; cDNA DKFZp686J23256 (from clone DKFZp686J23256)

241547_at

0.143

5.05E-09

H57166

Homo sapiens transcribed sequence with weak� similarity to protein ref:NP_062553.1 (H.sapiens)� hypothetical protein FLJ11267 [Homo sapiens]

1555765_a_at

0.142

0.000000031

GNG4

AF493872

guanine nucleotide binding protein (G protein), gamma 4

232541_at

0.141

6.3E-09

AK000106

Homo sapiens cDNA FLJ20099 fis, clone COL04544

1567706_at

0.138

3.59E-09

AF009316

Homo sapiens clone TUB2 Cri-du-chat region mRNA.

229725_at

0.135

0.0000424

FACL6

AV705292

fatty-acid-Coenzyme A ligase, long-chain 6

230689_at

0.134

6.31E-09

AA825243

Homo sapiens transcribed sequences

231814_at

0.134

0.00000213

AK025404

Homo sapiens cDNA FLJ26945 fis, clone RCT07769

206754_s_at

0.132

0.000018

CYP2B6

NM_000767

cytochrome P450, family 2, subfamily B, polypeptide 6

229659_s_at

0.129

0.000000786

PIGR

BE501712

polymeric immunoglobulin receptor

228834_at

0.128

3.65E-10

TOB1

BF240286

transducer of ERBB2, 1

241509_at

0.127

1.63E-08

AI637733

Homo sapiens transcribed sequences

231152_at

0.124

1.92E-08

AW452971

Homo sapiens transcribed sequence with moderate similarity to protein pir:I60307 (E. coli) I60307 beta-galactosidase, alpha peptide - Escherichia coli

227556_at

0.122

4.88E-11

NME7

AI094580

non-metastatic cells 7, protein expressed in (nucleoside-diphosphatekinase)

206143_at

0.116

0.000149

SLC26A3

NM_000111

solute carrier family 26, member 3

227736_at

0.116

0.0000185

AA553959

Homo sapiens clone DNA92219 RLLV1833 (UNQ1833) mRNA, complete cds

230461_s_at

0.115

2.85E-10

MUM-1

AI860326

melanoma ubiquitous mutated protein

1553970_s_at

0.11

0.0000329

CEL

BC042510

carboxyl ester lipase (bile salt-stimulated lipase)

207457_s_at

0.105

1.76E-09

LY6G6D

NM_021246

lymphocyte antigen 6 complex, locus G6D

205910_s_at

0.103

0.00000144

CEL

NM_001807

carboxyl ester lipase (bile salt-stimulated lipase)

228030_at

0.103

2.44E-11

RBM6

AI041522

RNA binding motif protein 6

1567045_at

0.102

7.89E-12

AF085866

Homo sapiens full length insert cDNA clone YN86A01

207412_x_at

0.0878

0.000000108

NM_001808

gb:NM_001808.1 /DB_XREF=gi:4502772 /GEN=CELL /FEA=FLmRNA /CNT=4 /TID=Hs.169271.0 /TIER=FL /STK=1 /UG=Hs.169271 /LL=1057 /DEF=Homo sapiens carboxyl ester lipase-like (bile salt-stimulated lipase-like) (CELL), mRNA. /PROD=carboxyl ester lipase-like (bile salt-stimulatedlipase-like) /FL=gb:NM_001808.1 gb:L14813.1

218963_s_at

0.0649

1.7E-09

KRT23

NM_015515

keratin 23 (histonedeacetylase inducible)

235652_at

0.0624

4.22E-10

SCML1

AI431345

sex comb on midleg-like 1 (Drosophila)