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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/)

From: Gene Expression Profiling in Hereditary, BRCA1-linked Breast Cancer: Preliminary Report

Affy_ID Gene Symbol Gene Title Fold change BRCA1(+)vs. sporadic limma rank
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