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Table 2 Breast cancer candidate serum biomarkers

From: Shotgun proteomics coupled to nanoparticle-based biomarker enrichment reveals a novel panel of extracellular matrix proteins as candidate serum protein biomarkers for early-stage breast cancer detection

# Accession number Uniprot ID Gene Description MW (kDa) Abundance (ppm) GO-CC Diff (%) Cases (%) Breast-specific Novel
1 124248516 P59665 DEFA1 Alpha-defensin 1 10 138   63 53   
2 4759070 Q16627 CCL14 Chemokine (C-C motif) ligand 14 isoform 1 precursor 11 83 ES 164 32   
3 4507065 P03973 SLPI Secretory leukocyte peptidase inhibitor precursor 14 9.52 EM 50 21 SPECIFIC  
4 4826898 P07737 PFN1 Profilin 1 15 207 EE 108 63 SPECIFIC  
5 5031635 P23528 CFL1 Cofilin 1 (non-muscle) 19 115 EM 133 58   
6 33946278 Q9Y281 CFL2 Cofilin 2 19 21.3 ES 80 37   
7 34850061 P62834 RAP1A RAP1A, member of RAS oncogene family* 21 0.35 M 100 26 SPECIFIC  
8 4885375 P16403 HIST1H1C Histone cluster 1, H1c 21 6.45 N 59 21 SPECIFIC  
9 4506413 P61224 RAP1B RAP1B, member of RAS oncogene family-like 21 0.67 M 167 74 SPECIFIC  
10 148227764 Q93045 STMN2 Superiorcervical ganglia, neural specific 10 21 1.59 EE 120 53 SPECIFIC  
11 33695095 P13224 GP1BB Glycoprotein Ib, beta polypeptide precursor 22 0.13 EE 133 21   
12 4504073 P61026 RAB10 Ras-related GTP-binding protein RAB10 22 0.11 M 145 58 SPECIFIC  
13 4507513 P35625 TIMP3 Tissue inhibitor of metalloproteinase 3 precursor 24 N/A EM 53 47   NOVEL
14 4507651 P67936 TPM4 Tropomyosin 4 isoform 2 29 125 M 173 21 SPECIFIC  
15 24234708 Q99697 PITX2 Paired-like homeodomain transcription factor 2 isoform b 35 N/A N 50 26   NOVEL
16 37550464 A6NMN3 FAM170B PREDICTED:family with sequence similarity 170,member B 36 3.16 M 67 21   
17 209862875 Q7Z4I7 LIMS2 LIM and senescent cell antigen-like domains 2 isoform 1 38 0.43 M 200 21 SPECIFIC  
18 156523970 P02765 AHSG Alpha-2-HS-glycoprotein 39 8613 ES 50 63 SPECIFIC  
19 156616273 P08567 PLEK Pleckstrin 40 49.4 ES 143 32   
20 4501889 P63267 ACTG2 Actin, gamma 2 propeptide 42 25.6 ES 114 100   
21 20127528 P63261 ACTG1 Actin, gamma 1 propeptide 42 0.78 M 120 32   
22 4501887 Q9HBI1 PARVB Parvin, beta isoform b 42 147 EM 112 100 SPECIFIC  
23 39725934 P36955 SERPINF1 Serine (or cysteine) proteinase inhibitor, clade F 46 3589 EM 111 21   
24 9966913 Q9P1U1 ACTR3B Actin-related protein 3-beta isoform 1 48 0.08 EE 200 26 SPECIFIC  
25 55770868 I0CMK4 TUBB4Q Tubulin, beta polypeptide 4, member Q 48 0.32   164 26   
26 17921989 Q6PEY2 TUBA3E Tubulin, alpha 3e 50 3.5 EE 94 47 SPECIFIC  
27 46409270 Q9H4B7 TUBB1 Beta tubulin 1, class VI 50 1.63 N 98 63 SPECIFIC  
28 4507729 Q9BQE3 TUBA1C Tubulin alpha 6 50 2.03 EE 57 21 SPECIFIC  
29 14210536 P68366 TUBA4A Tubulin, alpha 4a 50 0.53 N 89 37 SPECIFIC  
30 14389309 Q13885 TUBB2A Tubulin, beta 2 50 2.33 Mi 92 89 SPECIFIC  
31 13562114 Q9BUF5 TUBB6 Tubulin, beta 6 50 2.56 EE 72 68 SPECIFIC  
32 4503649 P00740 F9 Coagulation factor IX preproprotein 52 685 ES 200 21   
33 32483410 P38435 GC Vitamin D-binding protein precursor 53 4435 M 200 26 SPECIFIC  
34 21071030 Q9Y243 AKT3 AKT3 kinase isoform 2 54 8804 ES 150 32 SPECIFIC  
35 32307163 P04217 A1BG Alpha 1B-glycoprotein precursor 54 N/A M 57 42   
36 148746204 Q9Y251 HPSE Heparanase 61 0.02 ER 156 63   
37 13540563 Q9BXR6 CFHR5 Complement factor H-related 5 64 62.4 ER 67 26   
38 4504383 Q04756 HGFAC HGF activator preproprotein 71 534 ES 76 79   
39 41281905 Q86UX7 FERMT3 Fermitin family homolog 3 long form 76 4.34 ER 123 89 SPECIFIC  
40 54607120 P02788 LTF Lactotransferrin precursor 78 45.4 ES 51 63   
41 205277383 P26927 MST1 Macrophage stimulating 1 (hepatocyte growth factor-like) 82 269 ES 111 21 SPECIFIC  
42 119395709 P00488 F13A1 Coagulation factor XIII A1 subunit precursor 83 37.7 ER 63 21 SPECIFIC  
43 4504165 P06396 GSN Gelsolin isoform a precursor 86 8905 ES 120 21 SPECIFIC  
44 47078292 P05106 ITGB3 Integrin beta chain, beta 3 precursor 87 1.46 EE 160 63 SPECIFIC  
45 4501891 P12814 ACTN1 Actinin, alpha 1 isoform b 103 6.5 ES 160 58   
46 5453579 P13497 BMP1 Bone morphogenetic protein 1 isoform 3 precursor 111 1.38 EM 133 26 SPECIFIC  
47 88758615 P08514 ITGA2B Integrin alpha 2b preproprotein * 113 3.1 M 144 100 SPECIFIC  
48 7669550 P18206 VCL Vinculin isoform meta-VCL 124 94.5 M 153 21   
49 40317626 P07996 THBS1 Thrombospondin 1 precursor 129 41.4 EM 94 100 SPECIFIC  
50 12667788 P35579 MYH9 Myosin, heavy polypeptide 9, non-muscle 227 2.67 EM 200 21 SPECIFIC  
51 223029410 Q9Y490 TLN1 Talin 1 * 270 22.5 ER 131 89 SPECIFIC  
52 156938343 Q9Y4G6 TLN2 Talin 2 272 0.32 M 114 42 SPECIFIC  
53 105990514 O75369 FLNB Filamin B, beta (actin binding protein 278) 278 0.24 EM 86 32   
54 116063573 P21333 FLNA Filamin A, alpha isoform 1 * 280 9.63 EM 154 89 SPECIFIC  
55 15147337 O95071 UBR5 Ubiquitin protein ligase E3 component n-recognin 5 309 0.03 M 59 42   
56 33350932 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 532 0.04 EM 67 21 SPECIFIC  
  1. Abundance (ppm): protein abundance in plasma according to the PaxDB integrated plasma database. GO-CC Gene Ontology category cellular component, ES extracellular space, ER extracellular region, EM extracellular matrix, EE extracellular exosomes, M membrane, N nucleus, C cytoskeleton, Diff (%) relative difference in abundance (percentage) between cases and controls, Cases (%) percentage of breast cancer cases in which the protein is present, Breast-specific increased abundance in breast cancer patients sera only, Novel not yet reported in PaxDB (plasma, mass spectrometry)