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Table 3 Most frequent differentially expressed genes between ductal carcinoma in situ and invasive ductal carcinoma (IDC)

From: Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression

   Tag

Gene

Description

Locus link

Fold change

P value

IDC overexpressed genes

   TGGAAATGAC

COL1A1

Collagen type I, alpha 1

1277

315.4

0.0054

   ATGTGAAGAG

SPARC

Secreted protein, cysteine-rich (osteonectin)

6678

286.8

0.0003

   TTTGGTTTTC

COL1A2

Collagen type I, alpha 2

1278

210.9

0.0084

   TTGCTGACTT

COL6A1

Collagen type VI, alpha 1

1291

73.9

0.0023

   TTATGTTTAA

LUM

Lumican

4060

56.7

0.0011

   TTGGAGATCT

NDUFA4

NADH dehydrogenase (ubiquinone)

4697

56.4

0.0065

   CCACAGGGGA

COL3A1

Collagen type III, alpha 1

1281

49.4

0.0056

   ATCTTGTTAC

FN1

Fibronectin 1

2335

44.3

0.0031

   TTGTAATCGT

OAZ1

Ornithine decarboxylase antizyme 1

4946

38.6

0.0038

   TGTAATCAAT

HNRPA1

Heterogeneous nuclear ribonucleoprotein A1

3178

38.2

0.0039

   GGAAGCTAAG

OSF-2

Osteoblast specific factor 2 (fasciclin I-like)

10631

36.3

0.0005

   ACCTGTATCC

IFITM3

Interferon induced transmembrane protein 3

10410

34.3

0.0021

   GGAAATGTCA

MMP2

Matrix metalloproteinase 2

4313

29.1

0.0008

   TGCACTTCAA

SPARCL1

SPARC-like 1 (mast9, hevin)

8404

21.7

0.0050

   GGAACTTTTA

SULF2

Sulfatase 2

55959

19.8

0.0017

   CTGTTAGTGT

MDH1

Malate dehydrogenase 1

4190

18.5

0.0026

   TATGAATGCT

CSPG2

Chondroitin sulfate proteoglycan 2 (versican)

1462

18.2

0.0017

   TCCAAATCGA

VIM

Vimentin

7431

17.7

0.0014

   TGTAGTTTGA

SKP1A

S-phase kinase-associated protein 1A

6500

16.9

0.0013

   TAATAAACAG

ASAH1

n-Acylsphimgosine amidohydrolase

427

16.8

0.0085

   GCCTCCTCCC

EIF3k

Eukaryotic translation initiation factor 3

27335

16.8

0.0098

   GAAACAAGAT

PGK1

Phosphoglycerate kinase 1

5230

15.8

0.0006

   TGCTTTGGGA

TTC11

tetratricopeptide repeat domain 11

51024

15.8

0.0018

   GAAATCAAAA

SIGLEC5

Sialic acid binding Ig-like lectin 5

8778

14.7

0.0098

   ATGTAGTAGT

HNRPD

Heterogeneous nuclear ribonucleoprotein D

3184

14.7

0.0025

   GACCACCTTT

MFAP2

Microfibrillar-associated protein 2

4237

14.4

0.0000

   ACTTATTATG

DCN

Decorin

1634

13.9

0.0007

   TCTCTACCCA

APLP2

Amyloid beta (A4) precursor-like protein 2

334

13.7

0.0076

   TGCAATATGC

FBN1

Fibrillin 1

2200

13.5

0.0037

   ATTTCTTCAA

SFRP2

Secreted frizzled-related protein 2

6423

13.4

0.0030

   ATAAAAAGAA

CTSK

Cathepsin K (pycnodysostosis)

1513

13.0

0.0003

   GTACATTGTA

MGC15737

Hypothetical protein

85012

12.6

0.0011

   TGATGTTTGA

DAZAP2

DAZ associated protein 2

9802

12.5

0.0013

   TCCGTGGTTG

BASP1

Membrane attached signal protein 1

10409

12.1

0.0055

   ACTGCTTTAC

DKFZp564I1922

Adlican

25878

12.0

0.0086

   TCTGCAATGA

TINP1

Trasnforming growth factor beta-inducible nuclear protein 1

10412

12.0

0.0033

   GTTTCTTCCC

SELH

Selenoprotein H

2880636

11.8

0.0037

   AATATGCTTT

ATP6V1E1

ATPase

529

11.6

0.0009

   TTATGGATCT

SPON2

Spondin 2, extracellular matrix protein

10417

11.3

0.0003

   AAAATAAAGA

APEX1

Nuclease, multifunctional DNA repair enzyme

328

11.3

0.0099

   TGTGTGTTTG

HIF0

H1 histone family

3005

11.2

0.0029

   TATGTTTCAG

PTPN12

Protein tyrosine phosphatase

5782

11.1

0.0003

   ACCAAAGCCC

MGC9651

Hypothetical protein

114932

10.6

0.0075

   CAAGGATCTA

NICE-3

NICE-3 protein

25912

10.5

0.0057

   GACGTCTTAA

PSMA4

Proteasome subunit, alpha type

5685

10.3

0.0038

   CAGATAACAT

TOMM20

Translocase

9804

10.1

0.0064

   AACTCTTGAA

EIF3S3

Eukaryotic translation initiation factor 3

8667

10.0

0.0047

   TTCTTGGTGT

TRPS1

Trichorhinophalangeal syndrome I

7227

9.9

0.0042

   TGCCTTAGTA

DNAJC1

DNAJ homolog

64215

9.8

0.0040

   AGACAAGCTG

SFRS5

Splicing factor

6430

9.4

0.0015

   ACAAGAATTG

SYPL

Synaptophysin-like protein

6856

9.3

0.0027

   TACATCCGAA

MTPN

Myotrophin

136319

9.3

0.0013