Table 1

Selected genes up- or down-regulated in transgenic lungs

Affymetrix probe ID

Allele

Gene name

GenBank accession numbers

Fold change (transgenic/ wild-type)

p value


Genes down-regulated in transgenic lungs

Specialized cell markers

1418818_at

Aqp5

aquaporin 5

Mm.45580

NM_009701

96.1

0.009

1449015_at

Retnla

resistin like alpha

Mm.33772

NM_020509

37.5

0.004

1436996_x_at

Lyzs

lysozyme

Mm.45436

AV066625

36.5

6.82E-04

1451537_at

Chi3l1

chitinase 3-like 1

Mm.4376

BC005611

30.5

0.002

1429626_at

Sftpa

surfactant associated protein A

Mm.46062

AV024301

30.1

0.004

1420504_at

Slc6a14

solute carrier family 6 (neurotransmitter transporter)14

Mm.25770

AF320226

21.4

0.023

1419020_at

Gif

gastric intrinsic factor

Mm.456

NM_008118

19.7

0.003

1416456_a_at

Chia

chitinase, acidic

Mm.46418

BC011134

16.0

0.012

1423547_at

Lyzs

lysozyme

Mm.45436

AW208566

14.8

0.004

1419764_at

Chi3l3

chitinase 3-like 3

Mm.4571

NM_009892

13.6

0.013

1420378_at

Sftpd

surfactant associated protein D

Mm.1321

BC003705

12.0

2.10E-04

1448553_at

Myh7

myosin, heavy polypeptide 7, cardiac muscle, beta

Mm.155714

NM_080728

11.7

0.011

1455431_at

Slc5a1

solute carrier family 5 (sodium/glucose cotransporter)1

Mm.25237

AV371434

10.4

0.025

1437028_at

Sftpb

surfactant associated protein B

Mm.46033

AV025094

9.8

5.41E-04

1438696_at

Edn3

endothelin 3

Mm.9478

BB368452

7.0

0.016

1452543_a_at

Scgb1a1

secretoglobin, family 1A, member 1 (uteroglobin)

Mm.2258

X67702

5.2

0.014

1425291_at

Foxj1

forkhead box J1

Mm.4985

L13204

2.3

0.006

Genes up-regulated in transgenic lungs

Cell proliferation markers

1451417_at

Brca1

breast cancer 1

Mm.1889

U31625

9.5

0.004

1416969_at

Gtse1

G two S phase expressed protein 1

Mm.20858

NM_013882

5.9

7.58E-04

1416122_at

Ccnd2

cyclin D2

Mm.3141

NM_009829

3.5

1.27E-04

1422460_at

Mad2l1

MAD2 (mitotic arrest deficient, homolog)-like 1 (yeast)

Mm.43444

NM_019499

3.2

0.014

1425166_at

Rbl1

retinoblastoma-like 1 (p107)

Mm.2994

U27178

3.1

0.007

1417420_at

Ccnd1

cyclin D1

Mm.22288

BB538325

2.2

0.002

Transcription factors and Notch/Delta signaling

1421299_a_at

Lef1

lymphoid enhancer binding factor 1

Mm.200634

NM_010703

58.7

1.29E-04

1426552_a_at

Bcl11a

B-cell CLL/lymphoma 11A (zinc finger protein)

Mm.24020

BB772866

19.5

0.001

1417679_at

Gfi1

growth factor independent 1

Mm.2078

NM_010278

18.0

0.038

1449236_at

Dll3

delta-like 3 (Drosophila)

Mm.12896

AB013440

16.7

0.001

1424903_at

Smcy

selected mouse cDNA on the Y

Mm.1064

AF127244

10.8

0.006

1451835_at

Sox21

SRY-box containing gene 21

Mm.70950

AY069926

8.9

0.001

1449822_at

Atoh1

atonal homolog 1 (Drosophila)

Mm.57229

BC010820

7.4

0.001

1422914_at

Sp5

transacting transcription factor 5

Mm.155690

NM_022435

7.1

0.043

1448595_a_at

Rex3

reduced expression 3

Mm.14768

NM_009052

6.5

2.55E-04

1450164_at

Ascl1

achaete-scute complex homolog-like 1 (Drosophila)

Mm.10663

NM_008553

6.1

0.007

1460336_at

Ppargc1

peroxisome proliferative activated receptor, gamma, coactivator 1

Mm.10707

BB745167

5.7

0.039

1418055_at

Neurod4

neurogenic differentiation 4

Mm.10695

NM_007501

5.2

0.017

1424950_at

Sox9

SRY-box containing gene 9

Mm.46607

BI077717

5.1

0.019

1450339_a_at

Bcl11b

B-cell lymphoma/leukaemia 11B

Mm.116831

NM_021399

5.0

0.042

1460214_at

Pcp4

Purkinje cell protein 4

Mm.5023

NM_008791

4.5

0.012

1415811_at

Np95

nuclear protein 95

Mm.42196

BB702754

4.0

0.037

1419437_at

Sim2

single-minded 2

Mm.4775

NM_011377

3.9

0.03

1415810_at

Np95

nuclear protein 95

Mm.42196

NM_010931

3.9

0.017

1451255_at

Lisch7

liver-specific bHLH-Zip transcription factor

Mm.4067

BC004672

3.7

8.53E-04

1421951_at

Lhx1

LIM homeobox protein 1

Mm.4965

NM_008498

3.3

0.014

1417302_at

Rcor

RE1-silencing transcription factor (REST) co-repressor

Mm.22980

NM_054048

3.3

0.047

1422088_at

Lmyc1

Mus musculus, clone IMAGE:1528432, mRNA

Mm.198846

BI687857

3.0

0.001

1424942_a_at

Myc

myelocytomatosis oncogene

Mm.2444

BC006728

2.6

7.85E-04

1417155_at

Nmyc1

neuroblastoma myc-related oncogene 1

Mm.16469

BC005453

2.3

0.01

Specialized cell markers

Paneth cells

1450709_at

Defcr5

defensin related cryptdin 5

Mm.140173

NM_007851

844.0

0.003

1416905_at

Guca2

guanylate cyclase activator 2 (guanylin 2, intestinal, heatstable)

Mm.2614

NM_008190

322.2

0.001

1450631_x_at

Defcr6

defensin related cryptdin 6

Mm.246485

NM_007852

187.6

0.002

1427119_at

Spink4

serine protease inhibitor, Kazal type 4

Mm.25246

AV066321

99.5

1.18E-04

1418550_x_at

Defcr-rs1

defensin related sequence cryptdin peptide (paneth cells)

Mm.14269

NM_007844

22.8

0.007

1449478_at

Mmp7

matrix metalloproteinase 7

Mm.4825

NM_010810

9.0

0.002

1434852_at

Pla2g2e

phospholipase A2, group IIE

Mm.89936

AV228827

8.0

0.049

1427873_at

Defcr15

defensin related cryptdin 15

Mm.195047

U03065

3.4

0.019

1419254_at

Mthfd2

methylenetetrahydrofolate dehydrogenase (NAD+ dependent)

Mm.443

BG076333

2.6

0.004

Other cells

1417459_at

Dcpp

demilune cell and parotid protein

Mm.193062

NM_019910

285.6

8.59E-05

1450618_a_at

Sprr2a

small proline-rich protein 2A

Mm.6853

NM_011468

34.2

2.39E-04

1449279_at

Gpx2

glutathione peroxidase 2

Mm.57225

NM_030677

18.6

1.83E-04

1418931_at

Reg4

regenerating islet-derived family member 4

Mm.46306

NM_026328

15.4

0.001

1417370_at

Tff3

trefoil factor 3, intestinal

Mm.4641

NM_011575

12.0

0.001

1419127_at

Npy

neuropeptide Y

Mm.154796

NM_023456

7.2

0.033

1427355_at

Calca

calcitonin/calcitonin-related polypeptide, alpha

Mm.4361

X97991

5.0

0.019

1420965_a_at

Enc1

ectodermal-neural cortex 1

Mm.241073

BM120053

4.1

6.25E-04

1448290_at

Pap

pancreatitis-associated protein

Mm.2553

NM_011036

2.6

0.022

1417281_a_at

Mmp23

matrix metalloproteinase 23

Mm.29373

NM_011985

2.4

0.045

1422597_at

Mmp15

matrix metalloproteinase 15

Mm.7283

NM_008609

2.4

0.003

1421195_at

Cckar

cholecystokinin A receptor

Mm.3521

BC020534

2.1

0.004

Extracellular signaling factors

1416211_a_at

Ptn

pleiotrophin

Mm.3063

BF178348

25.5

7.50E-05

1454159_a_at

Igfbp2

insulin-like growth factor binding protein 2

Mm.141936

AK011784

24.9

0.007

1422324_a_at

Pthlh

parathyroid hormone-like peptide

Mm.28440

NM_008970

22.8

0.001

1422300_at

Nog

noggin

Mm.39094

NM_008711

12.8

9.64E-04

1423635_at

Bmp2

Bmp2

Mm.29877

AV239587

9.3

0.019

1448254_at

Ptn

pleiotrophin

Mm.3063

BC002064

7.9

7.62E-04

1418910_at

Bmp7

bone morphogenetic protein 7

Mm.595

NM_007557

6.2

0.004

1450922_a_at

Tgfb2

transforming growth factor, beta 2

Mm.18213

AW049938

4.5

1.06E-04

1420518_a_at

Igsf9

immunoglobulin superfamily, member 9

Mm.214530

AF317839

4.4

0.007

1450923_at

Tgfb2

transforming growth factor, beta 2

Mm.18213

BF144658

4.3

7.04E-04

1416006_at

Mdk

midkine

Mm.906

M34328

4.1

4.19E-04


For details of the Affymetrix GeneChip mouse 430A array analysis, which used RNA from three transgenic and three wild-type E18.5 lungs, see Materials and methods. Only selected genes taken from categories discussed in the text are shown. For the complete set of genes up- or down-regulated more than two-fold, and for the raw data, see Additional data files 2, 3 and 4.

Okubo and Hogan Journal of Biology 2004 3:11   doi:10.1186/jbiol3

Open Data