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Table 1 List of affected genes that had a significant change in their mRNA expression when TGFβ-differentiated T84 cells were compared to T84 cells grown solely in collagen I gel (= TGFβ-treated vs. control) and T84 cells differentiated by soluble factors secreted by mesenchymal cells were compared to T84 cells grown solely in collagen I gel (= 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

    

ratio

SD

p-value

FDR

ratio

SD

p-value

FDR

A

DHCR24: 24-dehydrocholesterol reductase

AA482324

1p33-p31.1

0.68

(±0.20)

0.699

0.733

1.01

(±0.14)

0.969

1.000

A

FDPS: farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)

T66907

T65907

1q22

0.29↓

0.57↓

(±0.24)

(±0.45)

0.180

0.148

0.291

0.272

1.43

1.06

(±1.32)

(±1.02)

0.807

0.499

1.000

1.000

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

A

CYP3A4: cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4

R91078

7q21.1

0.70

(±0.05)

0.372

0.479

0.88

(±0.18)

0.520

1.000

A

CYP2E: cytochrome P450, subfamily IIE (ethanol-inducible)

H50500

10q24.3-qter

0.58

(±0.31)

0.509

0.607

0.96

(±0.60)

0.991

1.000

A

CYP19A1: cytochrome P450, family 19, subfamily A, polypeptide 1

R32428

15q21.1

0.75

(±0.08)

0.744

0.812

1.09

(±0.14)

0.923

1.000

B

SDHB: succinate dehydrogenase complex, subunit B, iron sulfur (Ip)

AA463565

1p36.1-p35

0.43

(±0.20)

0.041

0.265

0.81

(±0.38)

0.570

1.000

B

UQCR: ubiquinol-cytochrome c reductase (6.4 kD) subunit

R46837

19p13.3

0.42

(±0.40

0.123

0.265

0.90

(±0.49)

0.629

1.000

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

D

EIF4E2: eukaryotic translation initiation factor 4E member 2

W01534

2q37

3.54

(±1.90)

0.390

0.495

0.90

(±0.71)

0.499

1.000

D

TFDP2: transcription factor Dp-2

AA465444

3q23

0.57

(±0.18)

0.036

0.265

0.97

(±0.33)

0.920

1.000

D

HNRPH1: heterogeneous nuclear ribonucleoprotein H1

W96114

5q35.3

0.53

(±0.24)

0.572

0.665

0.98

(±0.39)

0.739

1.000

D

ZNF193: zinc finger protein 193

AA252169

6p21.3

0.49

(±0.20)

0.102

0.265

0.96

(±0.68)

0.482

1.000

D

MYC: v-myc myelocytomatosis viral oncogene homolog (avian)

AA464600

8q24.12-q24.13

0.78

(±0.42)

0.156

0.275

0.91

(±0.27)

0.800

1.000

D

PRP18: pre-mRNA processing factor 18

H82325

10p12.33

0.52

(±0.28)

0.086

0.265

0.97

(±0.22)

0.791

1.000

D

TFDP1: transcription factor Dp-1

W33012

13q34

0.76

(±0.009)

0.858

0.898

0.99

(±0.26)

0.957

1.000

D

EIF2B2: eukaryotic translation initiation factor 2B, subunit 2 (beta, 39 kD)

R86304

14q24.3

0.64

(±0.19)

0.018

0.261

1.05

(±0.25)

0.765

1.000

D

ZNF161: zinc finger protein 161

AA232647

17q23.3

0.710.75

(±0.11) (±0.13)

0.339

0.445

0.94 1.08

(±0.31) (±0.11)

0.608

1.000 1.000

D

ZNF24: zinc finger protein 24 (KOX 17)

AA447098

18q12

0.73

(±0.07)

0.651

0.732

1.10

(±0.46)

0.712

1.000

D

ZNF358: Zinc finger protein 358

H20045

19p13

0.64

(±0.09)

0.304

0.411

0.93

(±0.30)

0.621

1.000

D

MRPL4: mitochondrial ribosomal protein L4

AA490981

19p13.2

0.66

(±0.13)

0.030

0.265

0.90

(±0.16)

0.503

1.000

D

RPS5: ribosomal protein S5

AA456616

19q13.4

0.66

(±0.13)

0.030

0.265

0.90

(±0.16)

0.503

1.000

D

EZF-2: endothelial zinc finger protein 2

R63318

19q13.43

0.58

(±0.22)

0.061

0.265

0.87

(±0.23)

0.374

1.000

D

ID1: inhibitor of DNA binding 1, dominant negative helix-loop-helix protein

AA457158

20q11

0.74

(±0.18)

0.210

0.317

1.06

(±0.13)

0.807

1.000

D

SF3A1 splicing factor 3a, subunit 1. 120 kD

T72698

22q12.2

0.71

(±0.13)

0.510

0.609

1.11

(±0.36)

0.967

1.000

E

CTNNBIP1: catenin, beta interacting protein 1

R78539

1p36.22

0.59

(±0.33)

0.205

0.313

1.23

(±0.91)

0.836

1.000

E

CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa

AA442092

3p21

0.65

(±0.06)

0.628

0.712

0.99

(±0.08)

0.948

1.000

E

WNT5A: wingless-type MMTV integration site family, member 5A

W49672

3p21-p14

0.72

(±0.19)

0.307

0.414

1.07

(±0.16)

0.899

1.000

E

TGFBR2: transforming growth factor, beta receptor II (70–80 kD)

AA487034

3p22

0.71

(±0.17)

0.450

0.555

1.06

(±0.14)

0.906

1.000

E

SIAH2: seven in absentia homolog 2 (Drosophila)

AA029041

3q25

0.65

(±0.13)

0.037

0.265

1.01

(±0.19)

0.948

1.000

E

PIK3R1: phosphoinositide-3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)

R54050

5q12-q13

0.61

(±0.11)

0.539

0.636

1.25

(±0.75)

0.832

1.000

E

PDGFRB: platelet-derived growth factor receptor, beta polypeptide

R56211

5q31-32

1.01

(±0.29)

0.957

0.973

1.23

(±0.16)

0.390

1.000

E

EGFR: epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)

R35665

W48713

7p12

0.470.75

(±0.04) (±0.13)

0.022 0.444

0.265 0.550

1.02 1.09

(±0.63) (±0.10)

0.806 0.693

1.000 1.000

E

IGF2: insulin-like growth factor 2 (somatomedin A)

N54596

11p15.5

0.570.63

(±0.16) (±0.17)

0.241 0.335

0.345 0.441

0.92 1.23

(±0.27) (±0.86)

0.565 0.912

1.000 1.000

E

SIAH1: seven in absentia homolog 1 (Drosophila)

AA447531

16q12

0.57

(±0.23)

0.055

0.265

0.97

(±0.55)

0.920

1.000

E

NLK: nemo-like kinase

R70769

17q11.2

0.55

(±0.24)

0.298

0.504

0.85

(±0.39)

0.499

1.000

E

SMAD4: SMAD, mothers against DPP homolog 4 (Drosophila)

AA456439

18q21.1

0.78

(±0.14)

0.186

0.296

1.00

(±0.23)

0.870

1.000

F

CTSS: cathepsin S

AA236164

1q21

0.53

(±0.04)

0.327

0.433

0.90

(±0.30)

0.580

1.000

F

PSMA3: proteasome (prosome, macropain) subunit, alpha type, 3

AA465593

14q23

0.58

(±0.19

0.319

0.426

1.11

(±0.68)

0.700

1.000

F

PSMB6: proteasome (prosome, macropain) subunit, beta type, 6

AA070997

17p13

0.76

(±0.16)

0.093

0.265

1.00

(±0.12)

0.972

1.000

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

H

KRT19:keratin 19

AA464250

17q21.2

13.90

(±16.73)

0.390

0.496

19.95

(±12.99)

0.499

1.000

J

LOC440582: similar to Peptidyl-prolyl cis-trans isomerase E (PPIase E) (Rotamase E) (Cyclophilin E) (Cyclophilin 33)

W17246

1p34.3

0.79

(±0.20)

0.290

0.397

1.11

(±0.14)

0.293

1.000

J

RP4-622L5: hypothetical protein RP4-622L5

T85191

1p36.11-p34.2

0.69

(±0.13)

0.066

0.265

1.11

(±0.37)

0.673

1.000

J

EST

T99671

2q36

0.66

(±0.18)

0.610

0.698

0.99

(±0.30)

0.770

1.000

J

FLJ12057

N77990

3q21

0.71

(±0.10)

0.394

0.501

1.01

(±0.26)

0.840

1.000

J

MGC2198

H81199

3q27-q28

0.57

(±0.25)

0.258

0.364

1.21

(±0.97)

0.727

1.000

J

EST

R74480

5

0.65

(±0.09)

0.148

0.272

0.93

(±0.55)

0.458

1.000

J

CCL28: chemokine (C-C motif) ligand 28

R38459

5p12

0.63

(±0.13)

0.288

0.395

1.06

(±0.41)

0.905

1.000

J

FCHO2: FCH domain only 2

H93842

5q13

1.03

(±0.54)

0.859

0.900

1.48

(±0.44)

0.277

1.000

J

Hypothetical gene supported by AK126569

N92035

5q23

0.52

(±0.20)

0.161

0.277

0.94

(±0.31)

0.577

1.000

J

SMG1: PI-3-kinase-related kinase SMG-1

W32907

6p12.3

0.70

(±0.22)

0.207

0.315

1.36

(±0.55)

0.259

1.000

J

cDNA DKFZp667D095

R26163

8p22

0.61

(±0.32)

0.118

0.265

1.10

(±0.59)

0.857

1.000

J

DPYS: hypothetical protein PRO2949

N73761

8q22

3.29↓

(±1.73)

0.513

0.611

0.85

(±0.54)

0.566

1.000

J

D12S2489E

AA397819

12p13.2-p12.3

0.66

(±0.06)

0.011

0.227

0.92

(±0.19)

0.678

1.000

J

ZNF629: Zinc finger protein 629

AA128587

16p11.1

0.55

(±0.15)

0.157

0.275

0.93

(±0.33)

0.533

1.000

J

cDNA FLJ32121 fis, clone PEBLM1000083

T69477

16q22

0.57

(±0.18)

0.124

0.265

0.85

(±0.25)

0.698

1.000

J

SFRS14: splicing factor, arginine/serine-rich 14

AA485539

19p12

0.70

(±0.17)

0.201

0.310

1.88

(±1.38)

0.995

1.000

J

PNPLA4: patatin-like phospholipase domain containing 4

AA449678

Xp22.3

0.58

(±0.09)

0.387

0.495

0.94

(±0.33)

0.634

1.000

J

LOC286467: hypothetical protein LOC286467

R95805

Xq26.1

2.85↑

(±1.02)

0.293

0.400

0.85

(±0.42)

0.530

1.000

  1. Genes are sorted by functional classification. A: Cellular metabolism (GO:0044237), Metabolism (other than energy metabolism), B: Generation of precursor metabolites and energy GO:0006091), 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), 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, was calculated by using t-test. FDR is the calculated Benjamin-Hochberg false discovery rate.