Table 4

Genes whose expression is decreased in DU-145 wtBRCA1 [versus control (Neo)] cell clones

Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix array (N = 1)
Transcription/Nuclear proteins
 AA857131HIV Tat-SF1 (Tat-specific factor 1)HTATSF10.29 ± 0.00 (2)
 W00975p300/CBP-associated factor (P/CAF)PCAF0.33 ± 0.09 (2)
 H27379Transcription elongation factor S-II (also called transcription elongation factor A)TCEA20.39 ± 0.00 (2)
 AA504265PINCH protein (LIM and senescent cell antigen like domains 1)LIMS10.41 ± 0.05 (2)
Stress response: oxidative stress and xenobiotic detoxification
 H86554Ceruloplasmin (ferroxidase) [multicopper oxidase, Fe & Cu homeostasis]CP0.18 ± 0.09 (3)0.030
 R33755GST π-1GSTP10.39 ± 0.00 (2)0.27
Replication/Cell cycle/DNA repair and metabolism
 AA042990Semaphorin E (protein associated with drug resistance)SEMA3C0.26 ± 0.13 (3)
 R19031Photolyase homologue [similar to Drosophila (6-4) photolyase]PH0.35 ± 0.10 (3)
 R10662DNA mismatch repair protein MLH1MLH10.37 ± 0.05 (2)
 N54344KIAA0074 (also called condensin subunit 2, Barren homologue protein 1)BRRN10.38 ± 0.09 (2)
 AA598887KIAA0178 (SMC1 structural maintenance of chromosomes 1-like 1)SMC1L10.42 ± 0.01 (2)
 AA683578Adenosine deaminaseADA0.42 ± 0.06 (2)0.28
 H94617Replication factor C (activator 1) 3 (38 kDa)RFC30.47 ± 0.00 (2)
 AA045192Retinoblastoma 1 (including osteosarcoma)RB10.49 ± 0.01 (2)
Signal transduction
 S75725Prostacyclin-stimulating factor (also known as IGFBP7)IGFBP70.21 ± 0.04 (2)
 AA055835Caveolin, caveolae protein, 22 kDaCAV10.31 ± 0.04 (3)
 AA284634Janus kinase 1 (a protein tyrosine kinase)JAK10.32 ± 0.09 (3)0.26
 AA425947RIG (regulated in glioma) [putative tumor suppressor, Ras-related gene]RIG0.32 ± 0.08 (3)0.29
 NM_015881Dickkopf homologue 3 (regulator of Wnt signaling)DKK30.37 ± 0.12 (2)
 AA418999Smad5 (a MAD-like protein, putative tumor suppressor)SMAD50.40 ± 0.04 (2)
 AA101793Lipid-activated, protein kinase PRK2PRK20.43 ± 0.06 (3)
Biosynthesis and metabolism
 AA599187Phosphoglycerate kinase 1 (hypoxia-inducible glycolytic enzyme)PGK10.32 ± 0.12 (2)0.35
 AA018372Liver glutamate dehydrogenaseGLUD10.36 ± 0.12 (2)
 AA489611Lactate dehydrogenase ALDHA0.40 ± 0.02 (2)
 H07926Mitochondrial 3-oxoacyl-CoA thiolase (acetyl-Coenzyme A acyltransferase 2)ACAA20.44 ± 0.02 (3)
Growth factor/Cytokine and receptors
 AA425028Human cytokine receptor EB13 (induced by EBV infection)EBI30.35 ± 0.05 (2)0.018
 AA424629Latent transforming growth factor β binding protein 2LTBP20.38 ± 0.11 (2)0.32
 R72075Human heregulin-β geneHRGA0.39 ± 0.01 (2)
 T64134Monocyte chemoattractant protein MCP-4 (= small inducible cytokine A13)CCL130.40 ± 0.05 (2)
 R39227Cytokine IK (also called IK factor, RER protein, red protein)IK0.40 ± 0.06 (2)
 H98636CD40L receptor precursor (CD40 antigen, member of TNF receptor family)CD400.41 ± 0.03 (2)
Cytoskeleton/Cell adhesion/Cell and organelle structure
 AA196000Actinin α-3ACTN30.31 ± 0.08 (3)
 AA669758Nucleophosmin (nucleolar phosphoprotein B23, numatrin)NPM10.38 ± 0.01 (2)
 AA452566Peroxisomal membrane protein 3 (35 D, Zellweger syndrome)PXMP30.46 ± 0.00 (2)0.47
Extracellular matrix
 W93163TNF-inducible protein TSG-6 precursor (a hyaluron binding protein)TNFAIP60.24 ± 0.10 (3)0.038
 AA134871Fibulin 1FBLN10.32 ± 0.07 (2)0.19
 AA418811Fibrillin 1 (Marfan syndrome)FBN10.44 ± 0.04 (2)0.092
Apoptosis/Cell death
 AA699697Tumor necrosis factorTNF0.18 ± 0.01 (2)0.043
 N69204Chromosome segregation gene homologue CAS (apoptosis susceptibility)CSE1L0.29 ± 0.03 (2)
 AA455413Ceramide glucosyltransferase (glucosylceramide synthase, GCS)UGCG0.40 ± 0.03 (3)
Inflammation/Immune and antiviral response/Histocompatibility
 AA625981FK506-binding protein 1 (12 kDa) [an immunophilin]FKBP10.40 ± 0.08 (4)0.066
 AA625981FK506-binding protein 1A (12 kDa) [an immunophilin]FKBP1A0.41 ± 0.08 (2)0.35
 AA419108Annexin IV (placental anticoagulant protein II)ANX40.40 ± 0.02 (2)0.36
Differentiation/Development/Tissue-specific expression or function
 AA400739SRY (sex-determining region Y)-box 9 (campomelic dysplasia, sex-reversal)SOX90.23 ± 0.03 (2)0.090
 H20758ZyginI (synaptogamin-interacting protein) [axonal growth and fasciculation]0.25 ± 0.06 (2)
 AA911661Homeo box B2HOXB20.29 ± 0.01 (2)0.045
 W58092Tropomyosin α chain (skeletal muscle)TPM10.31 ± 0.07 (3)0.17
 N79708Fragile X mental retardation protein 1 homologue FXR1FXR10.34 ± 0.12 (2)0.49
 AA598517Keratin 8KRT80.38 ± 0.07 (3)
Transmembrane/Membrane/Integrins
 N46419Synaptogyrin 3 (integral membrane protein, function unclear)SYNGR30.48 ± 0.02 (3)0.10
 H78244Intestinal and liver tetraspan membrane protein (il-TMP)TM4SF40.40 ± 0.06 (2)
RNA or protein processing/Protein modification and proteolysis
 AA476294Nucleolin (nuclear phosphoprotein) [synthesis & maturation of ribosomes]NCL0.27 ± 0.09 (2)
 AA143201Matrix metalloproteinase 1 (interstitial collagenase)MMP10.35 ± 0.07 (2)0.36
Function unknown
 R16604ESTs, weakly similar to TAL-60.14 ± 0.09 (2)
 AA455476Homo sapiens cDNA: FLJ22921 fis, clone KAT06711 (unnamed protein product)0.38 ± 0.06 (2)
 AA431438H. sapiens cDNA FLJ10500 fis, clone NT2RP20003690.38 ± 0.06 (2)
 R67042KIAA0265 (Kelch motif containing protein of unknown function)0.40 ± 0.00 (2)0.49