Table 2 Most differentially expressed genes in SSc-ILD and IPF compared to controls

Inhibitor of DNA binding 1, dominant negative helix-loop-helix protein

208937_s_at

25.5

917.5

36.1

0.00078

Interleukin 11

206924_at

23.6

717.8

30.4

0.015

Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein

207826_s_at

27.7

603.2

21.8

0.00051

Tetraspanin 13

217979_at

37.9

533.9

14.1

0.0033

Elastin

212670_at

43.7

396.9

9.1

0.0021

Xylosyltransferase I

213725_x_at

29.0

255.4

8.8

0.0024

Serpin peptidase inhibitor, clade E, member 1

202628_s_at

329.8

2473.2

7.5

0.0022

Basic helix-loop-helix family, member e40

201170_s_at

44.3

256.1

5.8

0.0014

Connective tissue growth factor

209101_at

467.9

2637.1

5.6

0.00068

Solute carrier family 7, member 5

201195_s_at

56.1

294.2

5.3

0.00022

Tropomyosin 1 (alpha)

206116_s_at

317.5

1619.6

5.1

0.0032

Phosphoribosyl pyrophosphate synthetase 1

208447_s_at

59.0

283.4

4.8

0.0036

Inhibin, beta A

210511_s_at

143.3

688.1

4.8

0.0012

Growth arrest and DNA-damage-inducible, beta

207574_s_at

68.1

306.6

4.5

0.0023

Coiled-coil domain containing 99

221685_s_at

85.1

373.3

4.4

0.0018

Cadherin 2, type 1, N-cadherin (neuronal)

203440_at

105.3

433.0

4.1

0.00095

Desmoplakin

200606_at

80.5

306.1

3.8

0.0016

Insulin-like growth factor binding protein 3

212143_s_at

408.6

1489.1

3.6

0.0068

Microtubule associated monoxygenase, calponin and LIM domain containing 2

212473_s_at

184.7

667.5

3.6

0.0039

Prostaglandin-endoperoxide synthase 1

215813_s_at

102.4

362.0

3.5

0.0083

Genes underexpressed in SSc-ILD vs. Control

Probe set ID

Control mean

SSc-ILD mean

Fold change

p value

Chemokine (C-X-C motif) ligand 10

204533_at

771.2

19.2

−40.1

0.00034

Chemokine (C-X-C motif) ligand 11

210163_at

179.9

5.0

−36.0

0.0027

Flavin containing monooxygenase 2 (non-functional)

211726_s_at

530.4

15.7

−33.7

0.017

Interferon-induced protein with tetratricopeptide repeats 2

217502_at

707.1

26.1

−27.1

0.0096

Vascular cell adhesion molecule 1

203868_s_at

835.2

32.2

−26.0

0.0049

Bone marrow stromal cell antigen 2

201641_at

315.8

12.5

−25.3

0.0081

Radical S-adenosyl methionine domain containing 2

213797_at

333.8

13.3

−25.1

0.0039

Interferon-induced protein 44-like

204439_at

370.7

15.4

−24.1

0.00033

Interferon-induced protein with tetratricopeptide repeats 1

203153_at

1744.2

82.6

−21.1

0.000039

2’,5’-oligoadenylate synthetase 1, 40/46 kDa

205552_s_at

374.6

18.3

−20.5

0.0014

Complement factor B

202357_s_at

837.0

42.6

−19.6

0.0036

Interferon-induced protein with tetratricopeptide repeats 3

204747_at

985.0

61.9

−15.9

0.00031

Chromosome 10 open reading frame 10

209183_s_at

208.8

13.6

−15.3

0.0062

Myxovirus resistance 1, interferon-inducible protein p78 (mouse)

202086_at

1361.9

91.2

−14.9

0.00012

Receptor (chemosensory) transporter protein 4

219684_at

196.4

13.3

−14.8

0.000091

Chemokine (C-C motif) ligand 11

210133_at

529.8

36.2

−14.6

0.0021

Retinoic acid receptor responder (tazarotene induced) 3

204070_at

239.4

17.2

−13.9

0.00024

Alcohol dehydrogenase 1B (class I), beta polypeptide

209613_s_at

268.9

19.8

−13.6

0.011

Secreted and transmembrane 1

213716_s_at

285.0

22.0

−13.0

0.0012

Interferon, alpha-inducible protein 6

204415_at

1196.6

93.7

−12.8

0.00043

Genes overexpressed in IPF vs. Control

Probe set ID

Control mean

IPF mean

Fold change

p value

Interleukin 11

206924_at

23.6

2374.9

100.6

0.0019

Inhibitor of DNA binding 1, dominant negative helix-loop-helix protein

208937_s_at

25.5

752.8

29.6

0.011

Tetraspanin 13

217979_at

37.9

1039.1

27.4

0.0052

NADPH oxidase 4

219773_at

12.3

323.6

26.4

0.016

Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein

207826_s_at

27.7

603.4

21.8

0.0025

Phospholamban

204939_s_at

25.7

460.1

17.9

0.035

Elastin

212670_at

43.7

766.9

17.6

0.0026

Xylosyltransferase I

213725_x_at

29.0

443.6

15.3

0.034

Galanin prepropeptide

214240_at

18.4

254.4

13.8

0.014

Cytokine receptor-like factor 1

206315_at

23.4

319.3

13.6

0.0098

Calponin 1, basic, smooth muscle

203951_at

83.0

1048.0

12.6

0.0024

Follistatin-like 3

203592_s_at

32.5

404.8

12.4

0.0048

CTP synthase

202613_at

39.5

454.7

11.5

0.000059

Endothelial cell-specific molecule 1

208394_x_at

10.2

116.8

11.4

0.031

Cadherin 6, type 2, K-cadherin (fetal kidney)

210602_s_at

26.2

298.4

11.4

0.00092

Proenkephalin

213791_at

33.7

366.7

10.9

0.00086

Adhesion molecule with Ig-like domain 2

222108_at

54.7

490.6

9.0

0.025

NUAK family, SNF1-like kinase, 1

204589_at

56.2

489.9

8.7

0.001

Tropomyosin 1 (alpha)

206117_at

30.9

261.7

8.5

0.0069

Inhibin, beta A

210511_s_at

143.3

1198.5

8.4

0.0023

Genes underexpressed in IPF vs. Control

Probe set ID

Control mean

IPF mean

Fold change

p value

Interferon-induced protein with tetratricopeptide repeats 1

203153_at

1744.2

5.4

−321.4

0.000033

Myxovirus resistance 1, interferon-inducible protein p78 (mouse)

202086_at

1361.9

8.8

−154.1

0.000096

Interferon, alpha-inducible protein 6

204415_at

1196.6

11.8

−101.2

0.00027

Chemokine (C-X-C motif) ligand 10

204533_at

771.2

9.5

−81.3

0.00031

Superoxide dismutase 2, mitochondrial

221477_s_at

2180.4

29.8

−73.2

<0.000001

Myxovirus resistance 2 (mouse)

204994_at

517.3

8.5

−60.6

0.00062

Interferon induced transmembrane protein 1 (9–27)

214022_s_at

3698.0

61.4

−60.3

<0.000001

Interferon-induced protein with tetratricopeptide repeats 3

204747_at

985.0

17.2

−57.2

0.00023

Pentraxin 3, long

206157_at

1415.2

35.2

−40.2

0.000016

Interferon-induced protein 44-like

204439_at

370.7

11.6

−31.9

0.0003

Complement component 3

217767_at

457.9

14.4

−31.8

0.000072

KIAA1199

212942_s_at

799.0

30.8

−26.0

0.00027

Interferon-induced protein 35

209417_s_at

455.6

18.1

−25.1

0.000062

Chemokine (C-X-C motif) ligand 1

204470_at

637.1

26.3

−24.2

<0.000001

Growth arrest-specific 1

204457_s_at

383.2

17.2

−22.3

0.000059

Signal transducer and activator of transcription 1, 91 kDa

209969_s_at

327.3

15.3

−21.4

0.000097

Chemokine (C-C motif) ligand 2

216598_s_at

2676.4

128.3

−20.9

0.00003

Interferon-induced protein 44

214453_s_at

335.0

17.0

−19.7

0.000027

Caspase 1 (interleukin 1, beta, convertase)

211367_s_at

180.6

10.0

−18.1

<0.000001

Tumor necrosis factor, alpha-induced protein 2

202510_s_at

404.2

22.6

−17.9

0.000003