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. 2013 Feb 8;12(5):1319–1334. doi: 10.1074/mcp.M112.024182

Table I. Top discrimination proteins between BRCA1-deficient and -proficient mammary tumors after short term cisplatin treatment.

NA means not applicable.

Description International protein index Gene ontology Human gene names Significant regulation in sensitive modela Fold change in sensitive modela p value in sensitive tumorsa Significant regulation in resistant modela Fold change in resistant modela p value in resistant tumorsa Top 30 proteinsb Top 12 proteinsc
Fatty-acid synthase IPI00113223 Lipid metabolic process FASN −1.3 0.0697 ↑ 1.7 0.0173 x x
Kii-67 protein IPI00124959 M phase MKI67 ↑ 1.5 0.0118 ↑ 7.1 0.0062 x x
Carbonic anhydrase 3 IPI00221890 Small molecule metabolic process CA3 ↓ −13.9 0.0000 ↑ 1.6 0.0089 x x
Fatty acid-binding protein, adipocyte IPI00116705 Lipid metabolic process FABP4 ↓ −2.6 0.0099 ↑ 1.6 0.0066 x x
Chromodomain-helicase-DNA-binding protein 4 IPI00396802 Chromosome organization CHD4 ↑ 1.6 0.0221 −1.0 0.4882 x x
Nuclear pore membrane glycoprotein 210 precursor IPI00342158 Establishment of protein localization NUP21 ↑ 1.9 0.0110 −2.0 0.2815 x x
Kinesin-like protein KIF11 IPI00130218 Mitotic spindle organization KIF11 ↑ 2.6 0.0106 ↑ 11.1 0.0281 x x
EH domain-containing protein-2 homolog IPI00402968 Organelle organization EHD2 −2.3 0.0996 ↑ 1.5 0.0470 x x
Glutathione S-transferase Mu 1 IPI00230212 Metabolic process GSTM1 ↓ −1.8 0.0252 1.2 0.2058 x x
Pyruvate carboxylase, full insert sequence IPI00114710 Lipid metabolic process PC ↓ −2.5 0.0144 ↑ 2.8 0.0261 x x
Perilipin IPI00223783 Lipid metabolic process PLIN1 −1.1 0.3851 ↓ −1.6 0.0334 x x
Condensation protein G isoform 1 IPI00122202 M phase NCAPG ↑ 1.9 0.0171 1.4 0.2403 x x
Major vault protein IPI00111258 mRNA transport MVP 2.0 0.2809 ↓ −3.3 0.0378 x
Small nuclear ribonucleoprotein Sm D2 IPI00119220 Nucleic acid metabolic process SNRPD ↑ 1.7 0.0320 −1.1 0.4066 x
γ-Synuclein IPI00271440 Regulation of neurotransmitter secretion SNCG −3.8 0.1126 ↑ 5.7 0.0045 x
Thymidylate kinase, full insert sequence IPI00831272 Deoxyribonucleotide biosynthetic process DTYMK ↑ 2.4 0.0189 −1.3 0.2717 x
Galactokinase 1 IPI00265025 Monosaccharide metabolic process GALK1 ↑ 1.6 0.0425 −1.2 0.2653 x
Isoform 1 of nuclear autoantigenic sperm protein IPI00130959 Chromosome organization NASP ↑ 2.0 0.0242 1.4 0.2464 x
Kinesin family member 23 IPI00407864 Mitotic spindle organization KIF23 ↑ 7.7 0.0030 1.7 0.3034 x
Flap structure-specific endonuclease 1, full insert IPI00410836 Nucleic acid metabolic process FEN1 ↑ 1.9 0.0350 2.0 0.0937 x
Tubulin-specific chaperone D IPI00461857 Macromolecule metabolic process TBCD ↑ 1.9 0.0447 −1.5 0.1893 x
Actin-binding protein anillin IPI00172197 Nuclear division ANLN ↑ 4.7 0.0078 7.0 0.0597 x
Ribonucleoside-diphosphate reductase M2 subunit IPI00112645 Deoxyribonucleotide biosynthetic process RRM2 ↑ 3.0 0.0249 2.0 0.2784 x
Isoform 1 of Mitochondrial 28 S ribosomal protein S29 IPI00275050 Cellular component organization DAP3 ↑ 2.6 0.0332 −1.0 0.4984 x
Isoform 1 of Borealin IPI00621765 M phase CDCA8 ↑ 3.5 0.0420 1.0 1.0000 x
Pre-mRNA-splicing factor ISY1 homolog IPI00469994 Nucleic acid metabolic process ISY1 ↑ 3.5 0.0431 −1.7 0.3100 x
39S ribosomal protein L24, mitochondrial precursor IPI00162769 Macromolecule biosynthetic process MRPL2 ↑ 5.0 0.0435 1.0 1.0000 x
Uncharacterized protein C6orf130 homolog IPI00154005 Purine nucleoside binding C6orf1 ↑ 100.0 0.0106 1.0 1.0000 x
Isoform 1 of protein FAM76B IPI00330763 NA FAM76 ↑ 100.0 0.0108 1.0 1.0000 x
Maternal embryonic leucine zipper kinase IPI00323045 Cellular macromolecule metabolic process MELK ↑ 100.0 0.0108 1.0 1.0000 x
Ligase I, DNA, ATP-dependent IPI00473314 Nucleic acid metabolic process LIG1 ↑ 2.7 0.0097 1.5 0.1850
Cation-independent mannose 6-phosphate receptor IPI00308971 Positive regulation of apoptosis IGF2R ↑ 1.5 0.0497 ↓ −1.6 0.0351
Glutathione S-transferase, θ3 IPI00116236 Glutathione metabolic process Gstt3 ↑ 2.9 0.0358 1.0 0.4967
Hsp90 co-chaperone Cdc37 IPI00117087 M phase CDC37 ↑ 2.1 0.0200 1.0 0.4925
Thyroid hormone receptor-associated protein 3 IPI00556768 Nucleic acid metabolic process THRAP ↑ 2.5 0.0143 1.0 0.4933
Isoform E of Fragile × mental retardation syndrome-related protein 1 IPI00122521 Regulation of translation FXR1 ↑ 100.0 0.0019 −1.3 0.2467
Isoform 2 of U2-associated protein SR140 IPI00467507 RNA processing U2SUR ↑ 2.4 0.0401 1.2 0.3749
Aggrecan core protein precursor IPI00119035 Proteolysis Acan 1.0 1.0000 ↓ −6.1 0.0054
mRNA turnover protein 4 homolog IPI00132578 Ribosome biogenesis MRTO4 ↑ 1.7 0.0457 1.2 0.3036
Isoform 7 of protein quaking IPI00130483 mRNA transport QKI −1.0 0.4981 ↑ 9.4 0.0004
Monocarboxylate transporter 4 IPI00118910 Monocarboxylic acid transport SLC16 ↑ 6.0 0.0272 −1.0 0.4990
Carbonic anhydrase 2 IPI00121534 Metabolic process CA2 ↓ −1.9 0.0353 1.1 0.4305
Myosin IE IPI00330649 Vasculogenesis MYO1E 1.3 0.2303 ↓ −1.7 0.0495
Niban-like protein IPI00330695 Negative regulation of apoptotic process FAM12 −1.4 0.3426 ↓ −1.8 0.0208
Vesicle-associated membrane protein-associated protein IPI00135655 Nucleotide catabolic process VAPB 3.0 0.1509 ↓ −6.0 0.0261
Isoform 1 of double strand break repair protein MRE11A IPI00118853 Nucleic acid metabolic process MRE11 ↑ 100.0 0.0106 −1.7 0.3082
Vesicle-associated membrane protein-associated protein IPI00125267 Cellular membrane fusion VAPA ↑ 1.9 0.0333 −1.3 0.1713
Isoform 2 of acetyl-CoA carboxylase 1 IPI00848443 Lipid metabolic process ACACA 1.5 0.2119 ↓ −2.7 0.0342
ADP-ribosylation factor interacting protein 1 IPI00466057 Establishment of localization in cell ARFIP1 ↑ 100.0 0.0057 −2.0 0.1596
Actin, cytoplasmic type 5 homolog IPI00221528 Nucleotide and ATP binding ACTBL 1.1 0.2369 ↑ 2.4 0.0200
Isoform 1 of translation initiation factor eIF-2B subunit IPI00124879 Metabolic process EIF2B4 ↓ −100.0 0.0116 3.0 0.1514
Pno1 RNA-binding protein PNO1 IPI00131909 RNA binding PNO1 ↓ −5.0 0.0444 1.0 0.4991
Isoform Long of Extracellular matrix protein 1 precursor IPI00122272 System development ECM1 −1.3 0.2637 ↓ −2.4 0.0106
Itih1 protein IPI00322867 Metabolic process ITIH1 ↓ −1.7 0.0130 1.1 0.2890
Ubiquitin-activating enzyme E1-like protein 2 IPI00226815 Proteolysis involved in cellular protein catabolic process UBA6 2.8 0.0556 ↓ −2.1 0.0358
Golgi resident protein GCP60 IPI00129907 Metabolic process ACBD3 ↓ −2.9 0.0442 7.0 0.0597

a The fold change and one-sided p value were calculated between protein levels in control and treated tumors.

b Top proteins with an average eight spectral count difference between treated tumors are given.

c Proteins with significant (p > 0.05, two-sided) difference between treated tumors are shown.