Table 2

Most frequent differentially expressed genes between normal breast epithelium and ductal carcinoma in situ (DCIS)

Tag

Gene

Description

Locus link

Fold change

P value

DCIS overexpressed genes

GTATTTAACT

PKD1-like

Polycystic kidney disease 1-like

79932

13.7

0.0100

CGGACTCACT

STARD10

START domain containing 10

10809

11.2

0.0086

GTGTTGGGGG

EPS8L2

EPS8-like 2

64787

9.6

0.0099

TTTCTGGAGG

KIAA0545

KIAA0545 protein

23094

8.6

0.0100

GATAAATTAA

FLJ14153

Hypothetical protein

64747

8.5

0.0055

GAGAAATATC

NP220

Nuclear protein

27332

8.0

0.0088

CCCTCTTTGG

LOC118487

mRNA similar to RIKEN cDNA 1110001019

118487

7.4

0.0037

CTGGGACTGA

LSM4

U6 small nuclear RNA associated (S. cerevisiae)

25804

6.4

0.0055

CTGGGCCAGC

VAMP5

Vesicle-associated membrane protein 5

10791

6.4

0.0068

GCCCTTTCTC

MRC2

Mannose receptor, C type 2

9902

5.8

0.0015

TCTTGATTTA

A2M

Alpha-2-macroglobulin

2

5.8

0.0083

TAGTTTGTGG

MSH2

MutS homolog 2, colon cancer

4436

5.6

0.0091

TCAGTGAACT

HPS4

Hermansky–Pudlak syndrome 4

89781

5.6

0.0100

GTTTATTCTT

FOXA1

Forkhead box A1

3169

5.3

0.0044

GCCGCTGCCA

PPP1R13B

Protein phosphatase 1

23368

4.3

0.0054

TAAAGTGTCT

PIGS

Phosphatidylinositol glycan, class S

94005

3.9

0.0100

DCIS underexpressed genes

GGGACGAGTG

TM4SF1

Transmembrane 4 superfamily member 1

4071

-442.6

0.0083

TAACAGCCAG

NFKBIA

Nuclear factor kappa light polypeptide gene

4792

-158.6

2.4 × 10^-6

CAACTAATTC

CLU

Clusterin

1191

-63.9

0.0036

GCCTTAACAA

PBEF

Pre-B-cell colony-enhancing factor

10135

-44.3

0.0020

GGGTTTTTAT

NSEP1

Nuclease sensitive element binding protein 1

4904

-36.2

0.0001

GACACGAACA

RASD1

RAS, dexamethasone-induce 1

51655

-31.4

0.0095

AAGATTGGTG

CD9

CD9 antigen (p24)

928

-29.6

0.0003

ACCAAATTAA

TNFRSF10B

Tumor necrosis factor receptor superfamily

8795

-29.4

0.0003

CTGGGCCTGA

LITAF

Lipopolysaccharide-induced tumor necrosis factor

9516

-28.9

0.0076

CTGCCATAAC

SBDS

Shwachman–Bodian–Diamond syndrome

51119

-24.2

0.0005

CACAGGCAAA

BZW1

Basic leucine zipper and W2 domains 1

9689

-22.1

0.0056

GTTCCCTGGC

FAU

Finkel–Biskis–Reilly murine sarcoma virus

2197

-22.1

0.0028

GTCTGCACCT

DKFZp547C1

Hypothetical protein

254851

-21.9

0.0087

TACGTTGCAG

GC20

Translocation factor sui1 homolog

10289

-21.8

0.0079

TGTAAAGATT

CCNL1

Cyclin L1

57018

-21.2

0.0008

TGTTAAGTTC

CRY1

Cryptochrome 1 (photolyase-like)

1407

-18.7

0.0091

GAAATAAAGT

FLJ21657

Hypothetical protein

64417

-18.5

0.0032

ATGGGCTTGA

SQRDL

Sulfide quinone reductase-like (yeast)

58472

-17.3

0.0061

TCAAGAAATT

PSME3

Proteasome activator subunit 3

10197

-15.7

0.0028

CCGTGGTCGT

FBL

Fibrillarin

2091

-15.3

0.0100

TGGAACAGGA

TGIF

Transforming growth factor beta-induced factor (TALE family homeobox)

7050

-12.2

0.0030

AATGCTGGCA

DNAJB6

DnaJ homolog, subfamily B, member 6

10049

-11.7

0.0065

AATGAGCAAC

GBP2

Guanylate binding protein 2, interferon-inducible

2634

-11.1

0.0082

GACCTATCTC

KIAA0992

Paladin

23022

-10.9

0.0092

AACTCTTGAA

EIF3S3

Eukaryotic translation initiation factor 3

8667

-10.6

0.0082

GGGATTTTGT

PMAIP1

Phorbol-12-myristate-13-acetate-induced protein 1

5366

-10.6

0.0091

AAAGCAAAAA

PTPN4

Protein tyrosine phosphatase, non-receptor type 4

5775

-10.4

0.0040

ACTGACTATC

NEU1

Sialidase 1 (lysosomal sialidase)

4758

-10.3

0.0095

TTCCAGTTCA

PDE4B

Phosphodiesterase 4B, camp-specific

5142

-9.9

0.0087

GAATGATTTC

ORF1-FL49

Putative nuclear protein

84418

-9.5

0.0070

GACTCGCTCC

HSJ001348

cDNA for differentially expressed CO16 gene

54742

-9.5

0.0072

TGGTTACAAA

NDEL1

Nude nuclear distribution gene E homolog like 1

81565

-8.9

0.0100

AGTATGAGGA

TNFAIP3

Tumor necrosis factor, alpha-induced protein 3

7128

-8.1

0.0083

CAGTTTAAAA

CRSP6

Cofactor required for Sp1 transcriptional activation

9440

-7.7

0.0100

Abba et al. Breast Cancer Res 2004 6:R499   doi:10.1186/bcr899