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Table 2 Characteristic of the gene expression experiments

From: Factors affecting the accuracy of a class prediction model in gene expression data

Disease

ID+

Medical question

Disease class

Cell/Tissue type

Affymetrix platform

Citation *

N

p

Ndeg

fc

cc

UC1

E-GEOD-14580

Response to treatment (non-/responder)

Inflammation

Colonic mucosal biopsies

HG U133 Plus 2.0

yes

24 (16,8)

4650

623

1.551

0.162

UC2

E-GEOD-21231

Response to treatment (non-/responder)

Inflammation

Blood

HG 1.0 ST

yes

40 (20,20)

3388

0

0.207

0.112

UC3

E-GEOD-36807

Diagnostic (UC/CD)

Inflammation

Intestinal biopsy

HG U133 Plus 2.0

no

28 (15,13)

6541

21

2.222

0.305

UC4

E-GEOD-23597

Response to treatment (non-/responder)

Inflammation

Colonic biopsy

HG U133 Plus 2.0

yes

14 (7,7)

4793

0

1.119

0.298

UC5

E-MTAB-331

Diagnostic (UC/CD)

Inflammation

CD8+ T cell

HG 1.0 ST and HG 1.1 ST

yes

59 (30,29)

1402

312

0.714

0.164

UC6

E-GEOD-9452

Diagnostic (with/without inflammation)

Inflammation

Colon

HG U133 Plus 2.0

yes

17 (8,9)

3702

2401

3.697

0.165

UC7

E-GEOD-6731

Diagnostic (UC/CD)

Inflammation

Colon

HG U95AV2

yes

30 (11,19)

1055

0

0.485

0.228

AST1

E-GEOD-27011

Diagnostic (mild/severe)

Inflammation

Blood

HG 1.0 ST

no

36 (19,17)

1293

39

0.302

0.113

AST2

E-GEOD-51392

Diagnostic (asthma/rhinitis)

Inflammation

Bronchial epithelial cells

HG U133 Plus 2.0

no

11 (6,5)

3969

0

1.805

0.171

AST3

E-GEOD-31773

Diagnostic (non/severe)

Inflammation

CD4 T cells

HG U133 Plus 2.0

no

12 (4,8)

18321

14488

16.964

0.317

DYS

E-GEOD-19419

Diagnosis (carrier/symp)

Infection

Blood

HG 1.0 ST

yes

45 (22,23)

2811

0

0.182

0.153

HIV1

E-GEOD-35864

Diagnostic (HIV/HIV with complication)

Infection

Basal ganglia

HG U133 Plus 2.0

no

18(6,12)

8737

0

1.14

0.346

HIV2

E-GEOD-14278

Prognostic (resistant/susceptible)

Infection

Peripheral blood

HG U133 Plus 2.0

no

18 (9,9)

11286

4

0.58

0.12

HIV3

E-GEOD-6740

Diagnostic (chronic/non chronic)

Infection

CD4 T cell

HG U133A

yes

15 (10,5)

865

5

0.74

0.168

PSO

E-GEOD-18948

Response to treatment (non-/responder)

Immune

Blood

HG U95

yes

16 (7,9)

1987

34

1.131

0.369

KD

E-GEOD-16797

Response to treatment (IVIG responsive /non)

Immune

Blood

HG U133 Plus 2.0

yes

12 (6,6)

11043

5

1.688

0.224

Dia1

E-GEOD-18732

Diagnostic (type 2 diabetes/intolerant)

Immune

Skeletal muscle

HG U133 Plus 2.0

no

71 (45,26)

2038

10

0.279

0.16

Dia2

E-CBIL-30

Diagnostic (diabetes type 2/abnormal glucose)

Immune

Skeletal muscle

HG U133A

yes

26 (18,8)

1749

0

0.269

0.435

ALZ1

E-GEOD-1297

Diagnostic (severe/not severe)

Degenerative

Hippocampus

HG U133A

yes

22 (7;15)

2295

13

0.693

0.287

ALZ2

E-MEXP-2280

Diagnostic (Alz/Pick's disease)

Degenerative

Medial temporal lobe

HG U133 Plus 2.0

yes

19 (7,12)

6899

1592

1.086

0.231

PARKI

E-GEOD-6613

Diagnostic (Parkinson/non-Parkinson)

Degenerative

Blood

HG U133A

yes

83 (50,33)

638

0

0.192

0.361

HF

E-GEOD-26887

Diagnostic (with/-out Diabetes)

Degenerative

Left ventricle cardiac biopsies

HG 1.0 ST

yes

19 (7,12)

2068

0

0.374

0.131

GAU

E-GEOD-21899

Diagnostic (type 1/ 3)

Hereditary

Skin

HG U133A 2.0

no

10 (5,5)

2017

4

1.807

0.143

CS

E-MEXP-2236

Diagnostic (Apert/Muenke)

Hereditary

Skin

HG U133 Plus 2.0

yes

20 (10;10)

5422

21

0.59

0.255

CF

E-GEOD-10406

Diagnostic (Chronic rhinosinusitis/+Cystic fibrosis)

Hereditary

Sinus mucosa

HG U133 Plus 2.0

no

15 (9,6)

7604

0

0.786

0.206

  1. + : The ArrayExpress accessing ID
  2. * : Paper availability
  3. Ndeg : The number of differentially expressed probesets
  4. fc : The average fold change from all probesets
  5. cc : The average within class correlation values from all probesets