Table 2 Genes differentiating between hereditary, BRCA1-positive breast cancers and sporadic tumours, selected by limma. Genes are ordered according to the fold change value and grouped into functional classes (according to Gene Ontology annotation, http://www.geneontology.org/)

Down-regulated in BRCA1(+)

   Cell proliferation and death

   202704_at

TOB1

transducer of ERBB2, 1

0.364

75

   243031_at

RTN4

Reticulon 4

0.421

71

   1556049_at

RTN4

reticulon 4

0.506

46

   215070_x_at

RABGAP1

RAB GTPase activating protein 1

0.731

97

   Cell signalling

   1553986_at

RASEF

RAS and EF-hand domain containing

0.25

49

   244181_at

PIK3R1

Phosphoinositide-3-kinase, regulatory subunit 1 (p85 alpha)

0.381

80

   238176_at

RAPGEF2

Rap guanine nucleotide exchange factor (GEF) 2

0.461

58

   229261_at

SOS1

Son of sevenless homolog 1 (Drosophila)

0.565

92

   215992_s_at

RAPGEF2

Rap guanine nucleotide exchange factor (GEF) 2

0.583

90

   207822_at

FGFR1

fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome)

0.704

82

   DNA and RNA

   233007_at

XRCC5

X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa)

0.667

22

   230651_at

THOC2

THO complex 2

0.414

45

   243908_at

ZNF638

Zinc finger protein 638

0.531

17

   218356_at

FTSJ2

FtsJ homolog 2 (E. coli)

0.699

57

   Metabolism

   239545_at

CAS1

O-acetyltransferase

0.331

26

   238563_at

TPRT

Trans-prenyltransferase

0.351

14

   215316_at

HIBADH

3-hydroxyisobutyrate dehydrogenase

0.539

30

   200961_at

SEPHS2

selenophosphate synthetase 2

0.576

72

   202282_at

HADH2

hydroxyacyl-Coenzyme A dehydrogenase, type II

0.585

2

   238813_at

ALAS2

Aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)

0.607

7

   232127_at

CLCN5

Chloride channel 5 (nephrolithiasis 2, X-linked, Dent disease)

0.626

33

   218124_at

RetSat

all-trans-13,14-dihydroretinol saturase

0.63

67

   Protein synthesis and degradation

   240146_at

CAPZA2

Capping protein (actin filament) muscle Z-line, alpha 2

0.267

28

   235138_at

PUM2

Vacuolar protein sorting 35 (yeast)

0.287

25

   1560926_at

PPP4R2

Protein phosphatase 4, regulatory subunit 2

0.323

88

   1554638_at

ZFYVE16

zinc finger, FYVE domain containing 16

0.43

56

   238303_at

SIMP

Source of immunodominant MHC-associated peptides

0.432

35

   232216_at

YME1L1

YME1-like 1 (S. cerevisiae)

0.443

87

   239175_at

AFTIPHILIN

Aftiphilin protein

0.486

4

   222499_at

MRPS16

mitochondrial ribosomal protein S16

0.537

62

   202347_s_at

HIP2

huntingtin interacting protein 2

0.565

8

   214843_s_at

USP33

ubiquitin specific protease 33

0.695

61

   Regulation of transcription

   1559949_at

TRPS1

Trichorhinophalangeal syndrome I

0.199

69

   210282_at

ZNF198

zinc finger protein 198

0.25

44

   202600_s_at

NRIP1

nuclear receptor interacting protein 1

0.282

70

   243792_x_at

PTPN13

Protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)

0.36

43

   222320_at

HRPT2

Hyperparathyroidism 2 (with jaw tumor)

0.403

11

   222544_s_at

WHSC1L1

Wolf-Hirschhorn syndrome candidate 1-like 1

0.408

18

   222313_at

CNOT2

CCR4-NOT transcription complex, subunit 2

0.412

15

   216022_at

WNK1

WNK lysine deficient protein kinase 1

0.414

31

   235409_at

MGA

MAX gene associated

0.443

40

   212881_at

PIAS4

protein inhibitor of activated STAT, 4

0.448

55

   227798_at

SMAD1

SMAD, mothers against DPP homolog 1 (Drosophila)

0.45

16

   213766_x_at

GNA11

guanine nucleotide binding protein (G protein), alpha 11 (Gq class)

0.487

39

   217550_at

ATF6

Activating transcription factor 6

0.518

94

   222180_at

YES1

V-yes-1 Yamaguchi sarcoma viral oncogene homolog 1

0.604

98

   218955_at

BRF2

BRF2, subunit of RNA polymerase III transcription initiation factor, BRF1-like

0.635

83

   212079_s_at

MLL

myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)

0.666

29

   213944_x_at

GNA11

guanine nucleotide binding protein (G protein), alpha 11 (Gq class)

0.693

59

   Other

   1559496_at

---

---

0.284

5

   234032_at

---

PRO1550

0.289

19

   242343_x_at

ZNF518

Zinc finger protein 518

0.309

68

   221543_s_at

SPFH2

SPFH domain family, member 2

0.322

6

   204148_s_at

ZP3 /// POMZP3

zona pellucida glycoprotein 3 (sperm receptor) /// POM (POM121 homolog, rat) and ZP3 fusion

0.324

65

   232489_at

FLJ10287

hypothetical protein FLJ10287

0.33

1

   236841_at

FLJ25222

CXYorf1-related protein

0.334

60

   227931_at

---

MRNA; cDNA DKFZp686D22106 (from clone DKFZp686D22106)

0.382

54

   238706_at

PAPD4

PAP associated domain containing 4

0.386

63

   221542_s_at

SPFH2

SPFH domain family, member 2

0.398

24

   231878_at

MVP

Major vault protein

0.412

12

   1564637_a_at

FLJ38426

hypothetical protein FLJ38426

0.47

52

   228971_at

---

---

0.476

95

   235970_at

MLR1

transcription factor MLR1

0.485

73

   230871_at

DHX30

DEAH (Asp-Glu-Ala-His) box polypeptide 30

0.5

99

   233228_at

ZNF407

Zinc finger protein 407

0.508

48

   237157_at

EVE1

SH3 domain protein D19

0.519

9

   215385_at

FTO

Fatso

0.527

41

   222496_s_at

FLJ20273

RNA-binding protein

0.528

42

   219001_s_at

WDR32

WD repeat domain 32

0.533

76

   235927_at

---

---

0.542

86

   1569813_at

STRN

striatin, calmodulin binding protein

0.549

66

   240939_x_at

---

---

0.557

79

   222642_s_at

TMEM33

transmembrane protein 33

0.558

81

   213984_at

SCC-112

SCC-112 protein

0.565

37

   234488_s_at

GCL /// GMCL1L

germ cell-less homolog 1 (Drosophila)

0.619

100

   201297_s_at

MOBK1B

MOB1, Mps One Binder kinase activator-like 1B (yeast)

0.626

96

   238660_at

WDFY3

WD repeat and FYVE domain containing 3

0.663

13

   212602_at

WDFY3

WD repeat and FYVE domain containing 3

0.708

47

   212602_at

WDFY3

WD repeat and FYVE domain containing 3

0.708

47

Up-regulated in BRCA1(+)

   Cell proliferation and death

   203139_at

DAPK1

death-associated protein kinase 1

1.896

74

   209074_s_at

TU3A

TU3A protein

2.865

89

   Cell signalling

   227125_at

IFNAR2

Interferon (alpha, beta and omega) receptor 2

1.791

23

   204613_at

PLCG2

phospholipase C, gamma 2 (phosphatidylinositol-specific)

2.083

20

   DNA and RNA

   203805_s_at

FANCA

Fanconi anemia, complementation group A /// Fanconi anemia, complementation group A

2.056

93

   Immune response

   211530_x_at

HLA-G

HLA-G histocompatibility antigen, class I, G

1.575

38

   205067_at

IL1B

interleukin 1, beta

1.809

78

   205671_s_at

HLA-DOB

major histocompatibility complex, class II, DO beta

2.37

3

   206407_s_at

CCL13

chemokine (C-C motif) ligand 13

2.89

10

   234764_x_at

IGLC2

Ig lambda chain V-region (VL-AIG) /// Immunoglobulin lambda variable 3-21

6.297

51

   Metabolism

   222046_at

ARS2

arsenate resistance protein ARS2

1.475

77

   204428_s_at

LCAT

lecithin-cholesterol acyltransferase

1.767

27

   208964_s_at

FADS1

fatty acid desaturase 1

1.9

64

   1555745_a_at

LYZ

lysozyme (renal amyloidosis)

7.787

36

   Regulation of transcription

   221010_s_at

SIRT5

sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae

1.378

32

   206090_s_at

DISC1

disrupted in schizophrenia 1

1.72

85

   Other

   237883_at

---

Transcribed locus

1.316

84

   213938_at

CAST

CAZ-associated structural protein

1.339

53

   1561759_at

---

Homo sapiens, clone IMAGE:5276804, mRNA

1.369

50

   218600_at

MGC10986

hypothetical protein MGC10986

1.46

21

   226410_at

LOC348180

hypothetical protein LOC348180

1.694

91

   241383_at

LOC201181

similar to hypothetical protein A930006D11

2.053

34