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. 2015 Apr 22;14(7):1814–1830. doi: 10.1074/mcp.M114.041335

Table I. Top 65 targets in proteomics study with statistically significant changes (with major focus on proteins related to lymph node positivity of grade 1 breast tumors) that were selected for analysis of gene expression at transcript level (right part of the table). Proteins with low number of observations (N≤10) in the proteomics study are in italics (see Experimental procedures for details). Agreements in statistically significant changes at protein and transcript levels are indicated in bold.

Protein level Annotation Acc. No. Gene symbol Protein name Proteomics
 Fold change Lower limit of CI Upper limit of CI p value Transcriptomics
 Rsd p value Protein function
N R
G1: N1–2/N0 P15086 CPB1 Carboxypeptidase B OS = Homo sapiens GN = CPB1 PE = 1 SV = 4 - [CBPB1_HUMAN] 12 4.34 2.86 6.59 0.002 6.74 5.53 0.025 Protease, Metalloprotease, Select calcium binding protein
G1: N1–2/N0 Q14161 GIT2 ARF GTPase-activating protein GIT2 OS = Homo sapiens GN = GIT2 PE = 1 SV = 2 - [GIT2_HUMAN] 3 1.53 1.49 1.56 0.028 1.15 0.11 0.138 Select regulatory molecule, G-protein modulator, Other G-protein modulator
G1: N1–2/N0 P31947 SFN 14–3-3 protein sigma OS = Homo sapiens GN = SFN PE = 1 SV = 1 - [1433S_HUMAN] 20 1.45 1.28 1.64 0.001 1.17 0.14 0.215 Miscellaneous function, Other miscellaneous function protein
G1: N1–2/N0 Q96BH1 RNF25 E3 ubiquitin-protein ligase RNF25 OS = Homo sapiens GN = RNF25 PE = 1 SV = 1 - [RNF25_HUMAN] 3 1.44 1.39 1.48 0.053 1.27 0.09 0.002 Molecular function unclassified
G1: N1–2/N0 Q9Y592 CCDC41 Coiled-coil domain-containing protein 41 OS = Homo sapiens GN = CCDC41 PE = 1 SV = 2 - [CCD41_HUMAN] 10 1.41 1.21 1.64 0.050 1.17 0.11 0.088 Molecular function unclassified
G1: N1–2/N0 Q9NZT2 OGFR Opioid growth factor receptor OS = Homo sapiens GN = OGFR PE = 1 SV = 3 - [OGFR_HUMAN] 18 1.39 1.24 1.56 0.002 1.13 0.09 0.124 Receptor, Other receptor
G1: N1–2/N0 Q96JB5 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 OS = Homo sapiens GN = CDK5RAP3 PE = 1 SV = 2 - [CK5P3_HUMAN] 10 1.33 1.14 1.55 0.082 1.02 0.10 0.877 Molecular function unclassified
G1: N1–2/N0 P63313 TMSB10 Thymosin beta-10 OS = Homo sapiens GN = TMSB10 PE = 1 SV = 2 - [TYB10_HUMAN] 32 1.32 1.18 1.49 0.003 1.25 0.14 0.050 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G1: N1–2/N0 Q04206 RELA Transcription factor p65 OS = Homo sapiens GN = RELA PE = 1 SV = 2 - [TF65_HUMAN] 18 1.30 1.16 1.47 0.020 1.22 0.09 0.012 Transcription factor, Other transcription factor, Nucleic acid binding
G1: N1–2/N0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 OS = Homo sapiens GN = PDLIM2 PE = 1 SV = 1 - [PDLI2_HUMAN] 8 1.30 1.21 1.40 0.009 1.29 0.11 0.007 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G1: N1–2/N0 P35442 THBS2 Thrombospondin-2 OS = Homo sapiens GN = THBS2 PE = 1 SV = 2 - [TSP2_HUMAN] 68 1.25 1.10 1.43 0.043 0.92 0.27 0.765 Cell adhesion molecule, Extracellular matrix, Extracellular matrix glycoprotein
G1: N1–2/N0 P16949 STMN1 Stathmin OS = Homo sapiens GN = STMN1 PE = 1 SV = 3 - [STMN1_HUMAN] 18 1.24 1.15 1.33 0.002 1.28 0.16 0.052 Miscellaneous function, Other miscellaneous function protein
G1: N1–2/N0 P67936 TPM4 Tropomyosin alpha-4 chain OS = Homo sapiens GN = TPM4 PE = 1 SV = 3 - [TPM4_HUMAN] 130 1.23 1.16 1.31 0.000 1.16 0.14 0.209 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G1: N1–2/N0 Q04917 YWHAH 14–3-3 protein eta OS = Homo sapiens GN = YWHAH PE = 1 SV = 4 - [1433F_HUMAN] 63 1.20 1.10 1.32 0.012 1.20 0.09 0.024 Miscellaneous function, Other miscellaneous function protein
G1: N1–2/N0 P01042 KNG1 Kininogen-1 OS = Homo sapiens GN = KNG1 PE = 1 SV = 2 - [KNG1_HUMAN] 24 0.60 0.45 0.79 0.050 1.12 0.09 0.186 Signaling molecule, Other signaling molecule, Select regulatory molecule, Protease inhibitor
G1: N1–2/N0 P00747 PLG Plasminogen OS = Homo sapiens GN = PLG PE = 1 SV = 2 - [PLMN_HUMAN] 38 0.74 0.64 0.85 0.007 NA NA NA Protease, Serine protease
G1: N1–2/N0 P06396 GSN Gelsolin OS = Homo sapiens GN = GSN PE = 1 SV = 1 - [GELS_HUMAN] 172 0.82 0.74 0.91 0.016 1.13 0.14 0.327 Select calcium binding protein, Other select calcium binding proteins, Cytoskeletal protein
G3: N1–2/N0 P22676 CALB2 Calretinin OS = Homo sapiens GN = CALB2 PE = 1 SV = 2 - [CALB2_HUMAN] 8 2.32 1.86 2.91 0.003 2.00 0.82 0.100 Select calcium binding protein, Calmodulin related protein
G3: N1–2/N0 Q9Y2M0 MTMR15 Coiled-coil domain-containing protein MTMR15 OS = Homo sapiens GN = MTMR15 PE = 2 SV = 4 - [MTMRF_HUMAN] 4 1.66 1.47 1.86 0.034 0.93 0.12 0.584 Molecular function unclassified
G3: N1–2/N0 P21926 CD9 CD9 antigen OS = Homo sapiens GN = CD9 PE = 1 SV = 4 - [CD9_HUMAN] 9 1.43 1.22 1.68 0.026 1.23 0.23 0.261 Cell adhesion molecule, Other cell adhesion molecule
G3: N1–2/N0 P58107 EPPK1 Epiplakin OS = Homo sapiens GN = EPPK1 PE = 1 SV = 1 - [EPIPL_HUMAN] 59 1.32 1.21 1.44 0.000 1.26 0.37 0.433 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G3: N1–2/N0 Q15063 POSTN Periostin OS = Homo sapiens GN = POSTN PE = 1 SV = 2 - [POSTN_HUMAN] 244 1.31 1.24 1.38 0.000 1.51 0.34 0.070 Cell adhesion molecule, Other cell adhesion molecule
G3: N1–2/N0 Q15582 TGFBI Transforming growth factor-beta-induced protein ig-h3 OS = Homo sapiens GN = TGFBI PE = 1 SV = 1 - [BGH3_HUMAN] 72 1.30 1.17 1.44 0.000 1.35 0.28 0.157 Signaling molecule, Cell adhesion molecule, Other cell adhesion molecule
G3: N1–2/N0 P60903 S100A10 Protein S100-A10 OS = Homo sapiens GN = S100A10 PE = 1 SV = 2 - [S10AA_HUMAN] 16 1.28 1.17 1.39 0.001 1.16 0.15 0.256 Select calcium binding protein, Calmodulin related protein
G3: N1–2/N0 P31949 S100A11 Protein S100-A11 OS = Homo sapiens GN = S100A11 PE = 1 SV = 2 - [S10AB_HUMAN] 74 1.26 1.19 1.33 0.000 1.19 0.18 0.279 Signaling molecule, Select calcium binding protein, Calmodulin related protein
G3: N1–2/N0 O15173 PGRMC2 Membrane-associated progesterone receptor component 2 OS = Homo sapiens GN = PGRMC2 PE = 1 SV = 1 - [PGRC2_HUMAN] 28 1.25 1.15 1.36 0.000 1.03 0.12 0.782 Receptor, Other receptor
G3: N1–2/N0 O43707 ACTN4 Alpha-actinin-4 OS = Homo sapiens GN = ACTN4 PE = 1 SV = 2 - [ACTN4_HUMAN] 167 1.25 1.21 1.29 0.000 1.04 0.13 0.767 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G3: N1–2/N0 P04083 ANXA1 Annexin A1 OS = Homo sapiens GN = ANXA1 PE = 1 SV = 2 - [ANXA1_HUMAN] 111 1.24 1.18 1.30 0.000 1.28 0.23 0.175 Signaling molecule, Select calcium binding protein, Annexin,Transfer/carrier protein
G3: N1–2/N0 P40763 STAT3 Signal transducer and activator of transcription 3 OS = Homo sapiens GN = STAT3 PE = 1 SV = 2 - [STAT3_HUMAN] 38 1.24 1.14 1.35 0.000 1.25 0.16 0.086 Transcription factor, Other transcription factor, Nucleic acid binding
G3: N1–2/N0 Q05682 CALD1 Caldesmon OS = Homo sapiens GN = CALD1 PE = 1 SV = 2 - [CALD1_HUMAN] 134 1.24 1.18 1.31 0.000 1.13 0.27 0.624 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G3: N1–2/N0 P55268 LAMB2 Laminin subunit beta-2 OS = Homo sapiens GN = LAMB2 PE = 1 SV = 2 - [LAMB2_HUMAN] 33 1.24 1.13 1.35 0.002 1.33 0.19 0.048 Extracellular matrix, Extracellular matrix linker protein
G3: N1–2/N0 P05556 ITGB1 Integrin beta-1 OS = Homo sapiens GN = ITGB1 PE = 1 SV = 2 - [ITB1_HUMAN] 29 1.22 1.14 1.30 0.000 1.28 0.14 0.034 Receptor, Other receptor, Cell adhesion molecule
N1–2/N0 P31944 CASP14 Caspase-14 OS = Homo sapiens GN = CASP14 PE = 1 SV = 2 - [CASPE_HUMAN] 10 1.74 1.32 2.29 0.064 2.30 1.41 0.179 Protease, Cysteine protease
N1–2/N0 Q96HF1 SFRP2 Secreted frizzled-related protein 2 OS = Homo sapiens GN = SFRP2 PE = 1 SV = 2 - [SFRP2_HUMAN] 8 1.48 1.23 1.79 0.097 1.31 0.24 0.148 Signaling molecule, Other signaling molecule
N1–2/N0 O43734 TRAF3IP2 Adapter protein CIKS OS = Homo sapiens GN = TRAF3IP2 PE = 2 SV = 2 - [CIKS_HUMAN] 28 1.37 1.21 1.55 0.002 1.23 0.10 0.012 Molecular function unclassified
N1–2/N0 Q14993 COL19A1 Collagen alpha-1(XIX) chain OS = Homo sapiens GN = COL19A1 PE = 1 SV = 3 - [COJA1_HUMAN] 10 1.36 1.27 1.46 0.001 1.20 0.77 0.779 Cell adhesion molecule, Extracellular matrix, Extracellular matrix structural protein
N1–2/N0 P06756 ITGAV Integrin alpha-V OS = Homo sapiens GN = ITGAV PE = 1 SV = 2 - [ITAV_HUMAN] 38 1.23 1.12 1.35 0.010 1.10 0.09 0.206 Cell adhesion molecule, Other cell adhesion molecule
N1–2/N0 P07951 TPM2 Tropomyosin beta chain OS = Homo sapiens GN = TPM2 PE = 1 SV = 1 - [TPM2_HUMAN] 80 1.21 1.12 1.32 0.002 1.11 0.13 0.353 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
N1–2/N0 P20962 PTMS Parathymosin OS = Homo sapiens GN = PTMS PE = 1 SV = 2 - [PTMS_HUMAN] 378 1.12 1.07 1.17 0.000 1.17 0.15 0.220 Molecular function unclassified
N1–2: G3/G1 P06702 S100A9 Protein S100-A9 OS = Homo sapiens GN = S100A9 PE = 1 SV = 1 - [S10A9_HUMAN] 30 1.83 1.43 2.34 0.001 4.27 2.15 0.006 Select calcium binding protein, Calmodulin related protein
N1–2: G3/G1 P51153 RAB13 Ras-related protein Rab-13 OS = Homo sapiens GN = RAB13 PE = 1 SV = 1 - [RAB13_HUMAN] 10 1.30 1.10 1.54 0.090 0.70 0.07 0.001 Select regulatory molecule, G-protein, Small GTPase
N1–2: G3/G1 P60709 ACTB Actin, cytoplasmic 1 OS = Homo sapiens GN = ACTB PE = 1 SV = 1 - [ACTB_HUMAN] 4 1.21 1.14 1.28 0.052 1.045 0.120 0.701 Cytoskeletal protein, Actin family cytoskeletal protein, Actin and actin related protein
N0: G3/G1 P08670 VIM Vimentin OS = Homo sapiens GN = VIM PE = 1 SV = 4 - [VIME_HUMAN] 881 0.74 0.73 0.76 0.000 1.076 0.119 0.511 Cytoskeletal protein, Intermediate filament
G3/G1 Q9NZT1 CALML5 Calmodulin-like protein 5 OS = Homo sapiens GN = CALML5 PE = 1 SV = 2 - [CALL5_HUMAN] 116 1.69 1.37 2.07 0.000 1.44 0.46 0.248 Select calcium binding protein, Calmodulin related protein
G3/G1 P23528 CFL1 Cofilin-1 OS = Homo sapiens GN = CFL1 PE = 1 SV = 3 - [COF1_HUMAN] 72 1.25 1.16 1.35 0.000 1.11 0.08 0.168 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
G3/G1 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein OS = Homo sapiens GN = SERBP1 PE = 1 SV = 2 - [PAIRB_HUMAN] 72 1.22 1.15 1.30 0.000 1.09 0.08 0.237 Nucleic acid binding, Other RNA-binding protein
G3/G1 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 OS = Homo sapiens GN = AHSA1 PE = 1 SV = 1 - [AHSA1_HUMA5N2] 52 1.22 1.10 1.35 0.003 1.206 0.093 0.017 Molecular function unclassified
G3/G1 P26447 S100A4 Protein S100-A4 OS = Homo sapiens GN = S100A4 PE = 1 SV = 1 - [S10A4_HUMAN] 151 1.28 1.18 1.38 0.000 1.206 0.125 0.074 Select calcium binding protein, Calmodulin related protein
G3/G1 P12830 CDH1 Cadherin-1 OS = Homo sapiens GN = CDH1 PE = 1 SV = 3 - [CADH1_HUMAN] 48 0.83 0.75 0.92 0.006 1.16 0.16 0.265 Cell adhesion molecule, Cadherin
G3/G1 Q13740 ALCAM CD166 antigen OS = Homo sapiens GN = ALCAM PE = 1 SV = 2 - [CD166_HUMAN] 28 0.84 0.73 0.96 0.050 0.43 0.07 0.000 Cell adhesion molecule, CAM family adhesion molecule
G3/G1 P02753 RBP4 Retinol-binding protein 4 OS = Homo sapiens GN = RBP4 PE = 1 SV = 3 - [RET4_HUMAN] 24 0.72 0.62 0.83 0.001 0.948 0.326 0.877 Transfer/carrier protein, Other transfer/carrier protein
G3/G1 Q96NY7 CLIC6 Chloride intracellular channel protein 6 OS = Homo sapiens GN = CLIC6 PE = 2 SV = 3 - [CLIC6_HUMAN] 231 0.47 0.42 0.53 0.000 0.082 0.030 0.000 Ion channel, Voltage-gated ion channel
ER+/ER- O95994 AGR2 Anterior gradient protein 2 homolog OS = Homo sapiens GN = AGR2 PE = 1 SV = 1 - [AGR2_HUMAN] 8 3.19 1.84 5.54 0.023 25.81 17.52 0.000 Miscellaneous function, Surfactant
ER+/ER- P50238 CRIP1 Cysteine-rich protein 1 OS = Homo sapiens GN = CRIP1 PE = 1 SV = 3 - [CRIP1_HUMAN] 5 3.07 2.31 4.06 0.010 5.29 1.30 0.000 Molecular function unclassified
ER+/ER- Q8TD06 AGR3 Anterior gradient protein 3 homolog OS = Homo sapiens GN = AGR3 PE = 1 SV = 1 - [AGR3_HUMAN] 10 2.21 1.70 2.88 0.002 72.69 46.42 0.000 Miscellaneous function, Surfactant
ER+/ER- P35443 THBS4 Thrombospondin-4 OS = Homo sapiens GN = THBS4 PE = 1 SV = 2 - [TSP4_HUMAN] 4 2.16 1.73 2.70 0.031 3.03 1.17 0.006 Cell adhesion molecule, Extracellular matrix, Extracellular matrix glycoprotein
ER+/ER- Q96S44 TP53RK TP53-regulating kinase OS = Homo sapiens GN = TP53RK PE = 1 SV = 2 - [PRPK_HUMAN] 4 1.57 1.43 1.71 0.014 1.28 0.19 0.110 Protease, Metalloprotease
ER+/ER- Q9BTC8 MTA3 Metastasis-associated protein MTA3 OS = Homo sapiens GN = MTA3 PE = 1 SV = 2 - [MTA3_HUMAN] 5 1.40 1.31 1.51 0.005 1.52 0.19 0.002 Transcription factor, Zinc finger transcription factor, Other zinc finger transcription factor
ER+/ER- Q9P2M7 CGN Cingulin OS = Homo sapiens GN = CGN PE = 1 SV = 2 - [CING_HUMAN] 11 1.38 1.21 1.56 0.004 2.54 0.60 0.000 Molecular function unclassified
ER+/ER- Q01995 TAGLN Transgelin OS = Homo sapiens GN = TAGLN PE = 1 SV = 4 - [TAGL_HUMAN] 59 1.26 1.22 1.30 0.000 0.94 0.19 0.759 Cytoskeletal protein, Actin family cytoskeletal protein, Non-motor actin binding protein
ER+/ER- P16070 CD44 CD44 antigen OS = Homo sapiens GN = CD44 PE = 1 SV = 2 - [CD44_HUMAN] 20 0.82 0.73 0.94 0.035 1.00 0.15 0.974 Receptor, Other receptor, Cell adhesion molecule, Cell junction protein
HER2+/HER2- P04626 ERBB2 Receptor tyrosine-protein kinase erbB-2 OS = Homo sapiens GN = ERBB2 PE = 1 SV = 1 - [ERBB2_HUMAN] 4 5.27 3.12 8.89 0.099 22.866 5.402 0.000 Receptor, Protein kinase receptor, Kinase, Protein kinase, Tyrosine protein kinase receptor
HER2+/HER2- Q9UGT4 SUSD2 Sushi domain-containing protein 2 OS = Homo sapiens GN = SUSD2 PE = 1 SV = 1 - [SUSD2_HUMAN] 20 2.92 1.80 4.77 0.013 7.97 3.39 0.000 Molecular function unclassified
HER2+/HER2- Q9UNE0 EDAR Tumor necrosis factor receptor superfamily member EDAR OS = Homo sapiens GN = EDAR PE = 1 SV = 1 - [EDAR_HUMAN] 7 0.66 0.56 0.78 0.058 0.69 0.27 0.346 Receptor, Other receptor
HER2+/HER2- P06703 S100A6 Protein S100-A6 OS = Homo sapiens GN = S100A6 PE = 1 SV = 1 - [S10A6_HUMAN] 20 0.76 0.68 0.84 0.004 0.73 0.16 0.170 Signaling molecule, Growth factor, Select calcium binding protein, Calmodulin related protein