Table 3 Differentially regulated genes (probe sets) in responders and nonresponders

Transcription/regulation of transcription

   TNFAIP3

AI738896

202643_s_at

TNFα-induced protein 3

1.1830

-

+

   TNFAIP3

NM_006290

202644_s_at

TNFα-induced protein 3

0.9956

-

+

   NFKBIA

AI078167

201502_s_at

NFκB enhancer in B-cell inhibitor alpha

0.4762

-

+

   RUNX1

L21756

211620_x_at

Runt-related transcription factor 1

0.3940

+

+

   JUN

BG491844

201464_x_at

c-jun proto-oncogene

0.1352

-

-

   ZFP36L2

AI356398

201367_s_at

Zinc finger protein 36, C3H type-like 2

0.1308

-

+

   SRRM2

AI655799

208610_s_at

Serine/arginine repetitive matrix 2

0.0081

+

-

   ASCL1

AW950513

213768_s_at

Achaete-scute complex-like 1

0.0444

-

-

   FOXO3A

AF041336

210655_s_at

Forkhead box O3A

0.0131

-

-

Immune response

   IL1B

NM_000576

205067_at

IL-1β

0.9716

-

+

   IL1B

M15330

39402_

IL-1β

0.9523

-

+

   CCL4

NM_002984

204103_at

Chemokine (C-C motif) ligand 4

0.8002

-

+

   CCL3

NM_002983

205114_s_at

Chemokine (C-C motif) ligand 3

0.4621

-

+

   CXCR4

AF348491

211919_s_at

Chemokine (C-X-C motif) receptor 4

0.2589

-

-

   CXCL2

M57731

209774_x_at

Chemokine (C-X-C motif) ligand 2

0.2532

-

+

   LTF

NM_002343

202018_s_at

Lactotransferrin

0.1884

-

-

   PBEF1

NM_005746

217739_s_at

Pre-B-cell colony-enhancing factor 1

0.0751

-

-

   IGHA1

S55735

217022_s_at

Immunoglobulin heavy constant alpha 1

0.0475

-

-

   IER3

NM_003897

201631_s_at

Immediate early response 3

0.0284

-

-

Receptors, cell surface antigens, cell adhesion

   ADAM12

AU145357

215613_at

ADAM metallopeptidase domain 12 (meltrin alpha)

0.5538

-

+

   ICAM1

AI608725

202637_s_at

Intercellular adhesion molecule 1 (CD54)

0.5399

-

-

   SCN2B

U87555

210364_at

Sodium channel, voltage-gated, type II, beta

0.2294

+

+

Signal transduction

   PDE4B

L20966

211302_s_at

Phosphodiesterase 4B, cAMP-specific

0.4374

-

+

   RAPGEF1

NM_005312

204543_at

Rap guanine nucleotide-exchange factor 1

0.2890

-

+

   MYO10

AI1561354

216222_s_at

Myosin X

0.2066

-

+

   PTPRD

NM_002839

205712_at

Protein tyrosine phosphatase, receptor type, D

0.1822

+

+

   SOCS1

AI056051

209999_x_at

Suppressor of cytokine signaling 1

0.1239

-

-

   PDE4B

NM_002600

203708_at

Phosphodiesterase 4B, cAMP-specific

0.0593

-

+

Metabolism

   LGALS13

NM_013268

220440_at

Lectin, galactose-binding, soluble, 13 (galectin 13)

0.5013

+

+

   SNCA

BG260394

204466_s_at

Synuclein, alpha

0.0568

-

-

   CHST3

AB017915

32094_at

Carbohydrate sulfotransferase 3

0.0366

-

+

Cellular and oxidative stress response

   CROP

AW089673

208835_s_at

Cisplatin resistance-associated overexpressed protein

0.7500

+

+

   PPP1R15A

NM_014330

202014_at

Protein phosphatase 1, regulatory (inhibitor) subunit 15A

0.6886

-

+

   PPP1R15A

U83981

37028_at

Protein phosphatase 1, regulatory (inhibitor) subunit 15A

0.5939

-

-

   DDIT4

M_019058

202887_s_at

DNA-damage-inducible transcript 4

0.2366

-

-

   SOD2

W46388

215223_s_at

Superoxide dismutase 2, mitochondrial

0.0724

-

-

   ADM

NM_001124

202912_at

Adrenomedullin

0.0459

-

+

Transport

   ATP2A3

AF068220

207521_s_at

ATPase, Ca²⁺ transporting, ubiquitous

0.227

-

-

   CHRND

NM_000751

207024_at

Cholinergic receptor, nicotinic, delta

0.1977

-

+

Protein binding

   PIGO

AC004472

214990_at

Phosphatidylinositol glycan, class O

0.5216

-

+

   IBRDC3

W27419

36564_at

IBR domain containing 3

0.1194

-

+

   EBP49

NM_001978

204505_s_at

Erythrocyte membrane protein band 4.9 (dematin)

0.0804

-

-

   FBX07

NM_012179

201178_at

F-box protein 7

0.0080

-

-

Unknown

   FSD1

NM_024333

219170_at

Fibronectin type III and SPRY domain containing 1

0.2935

-

+

   HCG4P6

AF036973

215974_at

HLA complex group 4 pseudogene 6

0.1518

-

+

   C20orf103

NM_013361

219463_at

Chromosome 20 open reading frame 103

0.0022

-

-