Skip to main content

Table 2 List of the 46 genes evincing a significant change in their mRNA expression both in TGFβ-treated compared to cultures grown in collagen I gel and medium (= TGFβ-treated vs. control) and IMR fibroblast soluble factor-differentiated cultures compared to cultures grown in collagen I gel and medium (= IMR-treated vs. control).

From: Gene expression in TGFbeta-induced epithelial cell differentiation in a three-dimensional intestinal epithelial cell differentiation model

Gene ontology class

Gene name

GenBank no

chromosomal location

TGFβ-treated vs. control

IMR-treated vs. control

ANOVA

    

ratio

SD

p-value

FDR

ratio

SD

p-value

FDR

p-value

A

CYP1B1:cytochrome P450, family 1, subfamily B, polypeptide 1

AA448157

2p21

0.66

(±0.26)

0.724

0.795

0.68

(±0.23)

0.716

1.000

0.669

A

UMPS: uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase)

AA426227

3q13

0.65

(±0.56)

0.365

0.464

0.68

(±0.45)

0.270

1.000

0.173

A

GM2A: GM2 ganglioside activator protein

AA453978

5q31.3-q33.1

0.36

(±0.26)

0.041

0.265

0.45

(±0.47)

0.292

1.000

0.279

A

AMD1: S-adenosylmethionine decarboxylase 1

R82299

6q21-q22

0.59

(±0.28)

0.054

0.265

0.80

(±0.50)

0.410

1.000

0.420

A

AHCY: S-adenosylhomocysteine hydrolase

AA485626

20cen-q13.1

0.65

(±0.23)

0.081

0.265

1.30

(±0.42)

0.210

1.000

0.347

A

HMOX1: heme oxygenase (decycling) 1

T71757

22q12

3.75

(±2.58)

0.693

0.769

0.70

(±0.54)

0.491

1.000

0.456

A

ALAS2: aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)

AA410346

Xp11.21

0.48

(±0.15)

0.010

0.225

0.80

(±0.41)

0.299

1.000

0.322

C

HIST1H2AC: histone 1, H2ac

AA453105

6p21.3

0.78

(±0.24)

0.369

0.477

0.78

(±0.28)

0.180

1.000

0.196

C

CDK6: cyclin-dependent kinase 6

H73724

7q21-q22

2.57

(±1.34)

0.418

0.525

0.61

(±0.34)

0.442

1.000

0.524

C

APC7: anaphase-promoting complex subunit 7

T67474

12q13.12

0.77

(±0.07)

0.141

0.269

0.80

(±0.13)

0.221

1.000

0.211

C

LASS4: LAG1 longevity assurance homolog 4 (S. cerevisiae)

AA025779

19p13.2

0.62

(±0.29)

0.282

0.388

0.73

(±0.33)

0.339

1.000

0.268

D

RLF: Rearranged L-myc fusion sequence

R26070

1p32

0.54

(±0.27)

0.467

0.571

0.77

(±0.29)

0.540

1.000

0.437

D

TCF7: transcription factor 7 (T-cell specific, HMG-box)

AA480071

5q31.1

0.76

(±0.49)

0.180

0.291

0.80

(±0.42)

0.297

1.000

0.258

D

TCF8: transcription factor 8 (represses interleukin 2 expression)

R22087

10p11.2

0.62

(±0.38)

0.371

0.479

0.74

(±0.39)

0.392

1.000

0.286

D

TCEA2: transcription elongation factor A (SII), 2

AA412500

20q13.33

0.61

(±0.36)

0.241

0.345

0.72

(±0.33)

0.161

1.000

0.157

E

TIE1: tyrosine kinase with immunoglobulin-like and EGF-like domains 1

AA432062

1p34-p33

0.68

(±0.20)

0.084

0.265

0.72

(±0.13)

0.070

1.000

0.077

E

GPA33: glycoprotein A33 (transmembrane)

AA055862

1q24.1

0.72

(±0.10)

0.679

0.756

0.80

(±0.16)

0.752

1.000

0.703

E

MAPKAPK2: mitogen-activated protein kinase-activated protein kinase 2

AA455056

1q32

0.61

(±0.10)

0.031

0.265

0.80

(±0.21)

0.385

1.000

0.488

E

PDZD2: PDZ domain containing 2

AA405458

5p13.2

0.62

(±0.07)

0.049

0.265

0.83

(±0.12)

0.350

1.000

0.428

E

PRL:prolactin

AA133920

6p22.2-p21.3

0.66

(±0.31)

0.368

0.470

0.69

(±0.29)

0.375

1.000

0.357

E

AKAP12:A kinase (PRKA) anchor protein (gravin) 12

AA478542

6q24-q25

0.75

(±0.41)

0.246

0.351

0.77

(±0.35)

0.256

1.000

0.287

E

STAM: signal transducing adaptor molecule (SH3 domain and ITAM motif) 1

AA485996

10p14-p13

0.56

(±0.26)

0.186

0.297

0.82

(±0.16)

0.382

1.000

0.396

E

CARP: cardiac ankyrin repeat protein, cytokine inducible nuclear protein C193

AA488072

10q23.31

0.77

(±0.16)

0.038

0.265

0.82

(±0.17)

0.073

1.000

0.080

E

MS4A1: membrane-spanning 4-domains, subfamily A, member 1 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide

N91385

11q12-q13.1

1.24

(±0.66)

0.612

0.699

1.63

(±0.62)

0.323

1.000

0.302

E

DRPLA: dentatorubral-pallidoluysian atrophy (atrophin-1)

H08642

12p13.31

0.65

(±0.42)

0.330

0.436

0.80

(±0.53)

0.364

1.000

0.256

E

PRKCB1: protein kinase C, beta 1/cDNA DKFZp761J0720

AA479102

16p11.2

1.70

(±0.75)

0.392

0.499

0.69

(±0.19)

0.376

1.000

0.557

E

FPR1: formyl peptide receptor 1

AA425249

19q13.4

0.44

(±0.25)

0.018

0.261

0.79

(±0.37)

0.371

1.000

0.436

E

PLCG1: phospholipase C, gamma 1 (formerly subtype 148)

R76365

20q12-q13.1

0.48

(±0.23)

0.050

0.265

0.81

(±0.48)

0.656

1.000

0.646

E

ARHGAP8: Rho GTPase activating protein 8

R69153

22q13.31

0.61

(±0.09)

0.017

0.261

0.80

(±0.23)

0.307

1.000

0.334

F

REN: renin

AA455535

1q32

0.44

(±0.32)

0.133

0.269

0.88

(±0.62)

0.385

1.000

0.326

F

PSMD2: proteasome (prosome, macropain) 26S subunit, non-ATPase, 2

AA455193

3q27.1

0.72

(±0.39)

0.341

0.448

0.73

(±0.50)

0.362

1.000

0.280

F

SERPINB6: serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6

AA410517

6p25

0.72

(±0.13)

0.369

0.477

0.74

(±0.27)

0.254

1.000

0.193

F

CRYAB: srystallin, alpha B

AA504943

11q22.3-q23.1

0.50

(±0.08)

0.096

0.265

0.72

(±0.30)

0.219

1.000

0.199

F

TGM2: transglutaminase 2 (C polypeptide. protein-glutamine-gamma-glutamyltransferase)

R97066

20q12

0.62

(±0.30)

0.171

0.284

0.73

(±0.24)

0.182

1.000

0.151

G

C5: somplement component 5

N73030

9q32-q34

0.74

(±0.09)

0.175

0.286

0.76

(±0.35)

0.206

1.000

0.122

H

COL5A1: collagen, type V, alpha 1

R75635

9q35

0.64

(±0.04)

0.618

0.704

0.78

(±0.28)

0.783

1.000

0.744

H

PNUTL2: peanut-like 2 (Drosophila),

T64878

17q22-q23

0.81

(±0.15)

0.408

0.514

1.15

(±0.08)

0.505

1.000

0.520

H

COL18A1: collagen, type XVIII, alpha 1

W07798

21q22.3

0.57

(±0.17)

0.164

0.279

0.84

(±0.22)

0.411

1.000

0.414

I

ATP6V0B: ATPase, H+ transporting, lysosomal 21 kD, V0 subunit c"

AA480826

1p32.3

0.69

(±0.05)

0.213

0.320

0.84

(±0.26)

0.244

1.000

0.276

I

BZAP45: basic leucine-zipper protein BZAP45

AA463591

2q33

0.46

(±0.25)

0.151

0.273

0.73

(±0.30)

0.259

1.000

0.226

I

ATP6IP1: ATPase, H+ transporting, lysosomal interacting protein 1

AA488715

Xq28

0.44

(±0.32)

0.205

0.312

0.84

(±0.48)

0.391

1.000

0.315

J

EST

R00591

4p16.1

3.20

(±1.50)

0.445

0.550

0.78

(±0.48)

0.455

1.000

0.572

J

RIPX: rap2 interacting protein x

R74171

4q21.1

0.62

(±0.20)

0.175

0.287

0.68

(±0.25)

0.251

1.000

0.222

J

EST

H63361

12q24.31

3.50

(±2.03)

0.271

0.376

0.66

(±0.26)

0.520

1.000

0.632

J

hypothetical protein BC017488

W93317

16q13

0.60

(±0.05)

0.006

0.192

0.80

(±0.24)

0.345

1.000

0.354

J

PTOV1 prostate tumour over expressed gene 1

AA486332

19q13.33

0.63

(±0.08)

0.090

0.265

0.84

(±0.17)

0.618

1.000

0.581

J

LOC286467: hypothetical protein LOC286467

R95805

Xq26.1

2.85

(±1.02)

0.293

0.400

0.85

(±0.42)

0.530

1.000

0.716

  1. Genes are sorted by functional classification. A: Cellular metabolism (GO:0044237), Metabolism (other than energy metabolism), C: Nucleic acid binding (GO:0003676), D: Transcription regulator activity (GO:0030528), E: Signal transducer activity (GO:0004871), Signal transduction (GO:0007165) and Cell communication (GO:0007154), F: Cellular macromolecule metabolism (GO:0044260), G: Inflammatory response (GO:0006954), H: Organelle organization and biogenesis (GO:0006996I), I: Transport (GO:0006810), J: Biological process unknown (GO:0000004), Upward arrow denotes up-regulated mRNA expression, downward arrow down-regulated mRNA expression, bold indicates genes that have significant alteration in gene expression. Ratio is mean value calculated from three separate microarray experiments; SD is the standard deviation between separate experiments. Statistic probability (p-value) for TGFβ-treated vs. control and for IMR-treated vs. control, were calculated by using t-test. FDR is the calculated Benjamin-Hochberg false discovery rate. All three groups, TGFβ-treated, IMR-treated and control, were compared together with ANOVA.