Table 1.
The important tumor-associated canonical pathways include antigen presentation pathway, mitochondrial dysfunction, GP6 signaling pathway, EIF2 signaling, and glutathione-mediated detoxification
| Pathway name | Protein | Coverage (%) | Unique peptides | PSMs | MW (kDa) | Calc. pI | Ratio (T/N) | p value (t test) |
|---|---|---|---|---|---|---|---|---|
| Antigen presentation pathway | HLA-A protein (fragment) (J7RE54_HUMAN) | 51.28 | 1 | 19 | 31.60 | 5.67 | 1.70 | 5.24E−03 |
| MHC class I antigen (fragment) (D0W033_HUMAN) | 37.73 | 1 | 12 | 31.57 | 5.94 | 2.69 | 4.15E−03 | |
| MHC class I antigen (fragment) (A0A0K0KRA3_HUMAN) | 47.51 | 1 | 11 | 21.19 | 7.02 | 4.12 | 5.31E−04 | |
| MHC class I antigen (fragment) (A0A0K0KSD4_HUMAN) | 48.62 | 1 | 13 | 21.22 | 7.87 | 1.82 | 5.58E−03 | |
| MHC class I antigen (fragment) (E3SWK8_HUMAN) | 53.04 | 1 | 15 | 21.12 | 7.37 | 2.21 | 2.77E−02 | |
| MHC class II antigen (fragment) (Q67AU1_HUMAN) | 31.18 | 1 | 4 | 10.84 | 5.10 | 3.58 | 6.74E−03 | |
| MHC class II antigen (fragment) (A0A0S2C388_HUMAN) | 25.4 | 5 | 7 | 28.68 | 7.43 | 2.01 | 1.13E−02 | |
| MHC class II antigen (fragment) (S6AP35_HUMAN) | 45.08 | 1 | 21 | 41.16 | 6.62 | 1.58 | 4.23E−02 | |
| MHC class II antigen (fragment) (A0A142L067_HUMAN) | 24.11 | 3 | 5 | 25.87 | 7.15 | 1.67 | 1.55E−02 | |
| HLA class II histocompatibility antigen, DR alpha chain (A0A0G2JMH6_HUMAN) | 32.68 | 2 | 47 | 28.60 | 5.00 | 1.82 | 8.26E−04 | |
| MHC class II antigen (fragment) (N1NSB5_HUMAN) | 52.81 | 2 | 10 | 10.89 | 6.52 | 1.84 | 1.55E−03 | |
| HLA-DRB5 protein (fragment) (A0A024F8S6_HUMAN) | 42.48 | 1 | 23 | 25.73 | 6.52 | 0.38 | 2.40E−04 | |
| MHC class Ib antigen (fragment) (I3RW89_HUMAN) | 25.42 | 3 | 11 | 33.78 | 5.40 | 1.60 | 3.08E−02 | |
| Protein disulfide-isomerase A3 (PDIA3_HUMAN) | 70.89 | 27 | 324 | 56.75 | 6.35 | 1.71 | 4.04E−03 | |
| Protein disulfide-isomerase A3 (fragment) (H7BZJ3_HUMAN) | 74.8 | 1 | 58 | 13.51 | 7.30 | 1.87 | 1.35E−03 | |
| Calreticulin variant (fragment) (Q53G71_HUMAN) | 62.32 | 21 | 156 | 46.89 | 4.45 | 1.98 | 1.19E−02 | |
| Antigen peptide transporter 2 (X5CMH5_HUMAN) | 28.31 | 17 | 36 | 77.65 | 7.85 | 1.60 | 1.20E−03 | |
| Mitochondrial dysfunction | Cytoplasmic aconitate hydratase (ACOC_HUMAN) | 13.27 | 10 | 13 | 98.34 | 6.68 | 0.65 | 6.04E−03 |
| Apoptosis-inducing factor 1, mitochondrial (AIFM1_HUMAN) | 46.66 | 24 | 158 | 66.86 | 8.95 | 1.59 | 2.76E−03 | |
| ATP synthase mitochondrial F1 complex assembly factor 1 (ATPF1_HUMAN) | 29.57 | 8 | 17 | 36.41 | 7.96 | 1.90 | 9.90E−03 | |
| ATP synthase mitochondrial F1 complex assembly factor 2 (ATPF2_HUMAN) | 21.45 | 5 | 10 | 32.75 | 7.09 | 1.54 | 1.57E−04 | |
| B cell CLL/lymphoma 2, isoform CRA_b (A0A024R2C4_HUMAN) | 4.88 | 1 | 1 | 22.32 | 6.96 | 0.31 | 3.30E−05 | |
| Cytochrome c oxidase copper chaperone (fragment) (H7C4E5_HUMAN) | 12.07 | 1 | 1 | 6.41 | 7.69 | 2.75 | 2.33E−03 | |
| Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (COX41_HUMAN) | 36.09 | 7 | 48 | 19.56 | 9.51 | 1.52 | 4.37E−03 | |
| Cytochrome c oxidase subunit 4 isoform 2, mitochondrial (COX42_HUMAN) | 5.85 | 1 | 1 | 20.00 | 9.63 | 0.21 | 6.28E−04 | |
| Cytochrome c oxidase subunit 6C (COX6C_HUMAN) | 52 | 7 | 30 | 8.78 | 10.39 | 1.54 | 5.97E−03 | |
| Cytochrome c oxidase subunit 7A2, mitochondrial (CX7A2_HUMAN) | 27.71 | 2 | 15 | 9.39 | 9.76 | 1.55 | 3.89E−02 | |
| Cytochrome c oxidase subunit 7A-related protein, mitochondrial (COX7R_HUMAN) | 54.39 | 4 | 8 | 12.61 | 9.42 | 1.88 | 5.33E−03 | |
| Cytochrome c (fragment) (C9JFR7_HUMAN) | 57.43 | 6 | 42 | 11.33 | 9.66 | 2.43 | 1.11E−03 | |
| Glutathione peroxidase 7 (GPX7_HUMAN) | 33.16 | 5 | 9 | 20.98 | 8.27 | 1.66 | 2.77E−04 | |
| Serine protease HTRA2, mitochondrial (HTRA2_HUMAN) | 13.1 | 4 | 7 | 48.81 | 10.07 | 1.58 | 8.22E−03 | |
| Amine oxidase (flavin-containing) B (AOFB_HUMAN) | 43.46 | 18 | 143 | 58.73 | 7.50 | 0.41 | 2.86E−04 | |
| Thioredoxin, mitochondrial (THIOM_HUMAN) | 36.75 | 3 | 18 | 18.37 | 8.29 | 1.52 | 5.11E−03 | |
| Cytochrome b-c1 complex subunit 6, mitochondrial (QCR6_HUMAN) | 51.65 | 5 | 18 | 10.73 | 4.44 | 1.59 | 1.63E−02 | |
| Voltage-dependent anion-selective channel protein 1 (VDAC1_HUMAN) | 81.27 | 17 | 431 | 30.75 | 8.54 | 1.55 | 4.97E−03 | |
| GP6 signaling pathway | Disintegrin and metalloproteinase domain-containing protein 10 (ADA10_HUMAN) | 10.83 | 7 | 9 | 84.09 | 7.77 | 1.57 | 3.42E−04 |
| EIF2 signaling | Collagen alpha-1(X) chain (COAA1_HUMAN) | 1.91 | 1 | 1 | 66.12 | 9.67 | 0.24 | 2.71E−04 |
| Collagen alpha-1(XVI) chain (COGA1_HUMAN) | 1.81 | 3 | 4 | 157.65 | 7.84 | 0.43 | 7.50E−04 | |
| Collagen alpha-1(I) chain (CO1A1_HUMAN) | 14.96 | 7 | 87 | 138.86 | 5.80 | 0.30 | 8.28E−05 | |
| Collagen, type I, alpha 1, isoform CRA_a (D3DTX7_HUMAN) | 18.53 | 2 | 61 | 84.69 | 6.24 | 0.36 | 5.47E−05 | |
| Collagen alpha-2(I) chain (A0A087WTA8_HUMAN) | 13.27 | 15 | 55 | 129.07 | 9.01 | 0.29 | 1.84E−03 | |
| Collagen alpha-1(II) chain (CO2A1_HUMAN) | 3.03 | 3 | 3 | 141.70 | 6.92 | 0.17 | 7.01E−04 | |
| Collagen alpha-1(III) chain (CO3A1_HUMAN) | 6.41 | 9 | 21 | 138.48 | 6.61 | 0.30 | 6.85E−04 | |
| Collagen alpha-2(IV) chain (CO4A2_HUMAN) | 6.43 | 7 | 18 | 167.45 | 8.66 | 0.39 | 4.18E−03 | |
| Collagen, type V, alpha 2, isoform CRA_b (D3DPH5_HUMAN) | 2.14 | 2 | 2 | 86.03 | 6.06 | 0.24 | 3.59E−03 | |
| Collagen alpha-1(VI) chain (CO6A1_HUMAN) | 32.78 | 27 | 57 | 108.46 | 5.43 | 0.40 | 1.54E−03 | |
| Collagen alpha-2(VI) chain (CO6A2_HUMAN) | 18.84 | 18 | 50 | 108.51 | 6.21 | 0.44 | 5.27E−04 | |
| Collagen alpha-3(VI) chain (E7ENL6_HUMAN) | 31.1 | 1 | 165 | 277.95 | 8.18 | 0.37 | 4.07E−04 | |
| Collagen alpha-6(VI) chain (CO6A6_HUMAN) | 0.71 | 1 | 2 | 247.02 | 6.89 | 0.40 | 2.11E−03 | |
| Collagen alpha-1(VIII) chain (CO8A1_HUMAN) | 4.84 | 3 | 8 | 73.32 | 9.61 | 0.33 | 9.61E−04 | |
| Inositol 1,4,5-trisphosphate receptor type 1 (ITPR1_HUMAN) | 12.8 | 23 | 48 | 313.73 | 6.04 | 0.59 | 6.55E−05 | |
| Laminin subunit alpha-2 (A0A087WYF1_HUMAN) | 3.85 | 10 | 12 | 343.20 | 6.37 | 0.58 | 3.10E−03 | |
| Laminin subunit gamma-2 (LAMC2_HUMAN) | 4.02 | 4 | 4 | 130.89 | 6.19 | 1.60 | 4.91E−03 | |
| Protein kinase C (A0A169TED2_HUMAN) | 11.61 | 6 | 10 | 76.64 | 7.47 | 0.57 | 4.56E−03 | |
| B cell CLL/lymphoma 2, isoform CRA_b (A0A024R2C4_HUMAN) | 4.88 | 1 | 1 | 22.32 | 6.96 | 0.31 | 3.30E−05 | |
| Eukaryotic translation initiation factor 3 subunit C (B4E2Z6_HUMAN) | 19.52 | 11 | 20 | 90.48 | 5.71 | 0.62 | 6.44E−04 | |
| Eukaryotic translation initiation factor 3 subunit D (EIF3D_HUMAN) | 12.77 | 5 | 10 | 63.93 | 6.05 | 0.64 | 3.21E−03 | |
| Eukaryotic translation initiation factor 3 subunit E (EIF3E_HUMAN) | 26.29 | 11 | 18 | 52.19 | 6.04 | 0.65 | 1.78E−04 | |
| Eukaryotic translation initiation factor 3 subunit F (B4DMT5_HUMAN) | 31.27 | 8 | 14 | 33.22 | 5.59 | 0.64 | 1.04E−03 | |
| Eukaryotic translation initiation factor 3 subunit G (fragment) (K7ER90_HUMAN) | 9.25 | 2 | 2 | 25.43 | 5.49 | 0.61 | 7.81E−04 | |
| Eukaryotic translation initiation factor 3 subunit H (A0A087WZK9_HUMAN) | 22.92 | 6 | 9 | 39.56 | 6.39 | 0.58 | 3.64E−03 | |
| Eukaryotic translation initiation factor 3 subunit I (EIF3I_HUMAN) | 17.23 | 6 | 9 | 36.48 | 5.64 | 0.65 | 1.56E−03 | |
| Eukaryotic translation initiation factor 3 subunit K (K7ES31_HUMAN) | 20.44 | 2 | 4 | 15.86 | 6.74 | 0.65 | 5.63E−03 | |
| Eukaryotic translation initiation factor 3 subunit L (B4DQF6_HUMAN) | 6.97 | 4 | 7 | 62.65 | 6.16 | 0.63 | 1.71E−03 | |
| Eukaryotic initiation factor 4A-II (E7EQG2_HUMAN) | 44.48 | 6 | 32 | 41.26 | 5.64 | 0.62 | 1.08E−02 | |
| 40S ribosomal protein S30 (RS30_HUMAN) | 16.95 | 1 | 2 | 6.64 | 12.15 | 0.53 | 3.97E−03 | |
| 78 kDa glucose-regulated protein (GRP78_HUMAN) | 56.73 | 35 | 376 | 72.29 | 5.16 | 1.77 | 1.87E−04 | |
| Polypyrimidine tract binding protein 1, isoform CRA_b (A6NLN1_HUMAN) | 12.71 | 5 | 14 | 56.48 | 9.38 | 0.50 | 9.42E−04 | |
| 60S ribosomal protein L12 (RL12_HUMAN) | 44.85 | 5 | 12 | 17.81 | 9.42 | 0.57 | 1.62E−03 | |
| 60S ribosomal protein L23a (RL23A_HUMAN) | 31.41 | 5 | 13 | 17.68 | 10.45 | 0.65 | 7.46E−03 | |
| 60S ribosomal protein L9 (RL9_HUMAN) | 39.58 | 7 | 20 | 21.85 | 9.95 | 0.64 | 2.02E−03 | |
| RPLP1 protein (Q6FG99_HUMAN) | 44.74 | 2 | 8 | 11.56 | 4.37 | 0.56 | 1.05E−03 | |
| 40S ribosomal protein S12 (RS12_HUMAN) | 53.79 | 7 | 21 | 14.51 | 7.21 | 0.65 | 1.54E−03 | |
| 40S ribosomal protein S19 (RS19_HUMAN) | 39.31 | 6 | 25 | 16.05 | 10.32 | 0.56 | 3.77E−04 | |
| 40S ribosomal protein S20 (RS20_HUMAN) | 25.21 | 3 | 10 | 13.36 | 9.94 | 0.64 | 5.19E−05 | |
| 40S ribosomal protein S21 (Q8WVC2_HUMAN) | 12.35 | 1 | 3 | 8.84 | 8.50 | 0.63 | 3.09E−03 | |
| 40S ribosomal protein S28 (RS28_HUMAN) | 46.38 | 3 | 8 | 7.84 | 10.70 | 0.54 | 5.04E−03 | |
| 40S ribosomal protein S29 (A0A087WTT6_HUMAN) | 13.21 | 1 | 2 | 6.11 | 9.14 | 0.66 | 3.27E−03 | |
| 40S ribosomal protein S3 (RS3_HUMAN) | 65.43 | 15 | 46 | 26.67 | 9.66 | 0.62 | 5.61E−05 | |
| Ras-related protein R-Ras (RRAS_HUMAN) | 29.36 | 4 | 11 | 23.47 | 6.93 | 0.64 | 1.88E−02 | |
| Ras-related protein R-Ras2 (RRAS2_HUMAN) | 18.63 | 2 | 7 | 23.38 | 6.01 | 0.66 | 6.54E−03 | |
| Glutathione-mediated detoxification | Glutathione S-transferase kappa 1 (GSTK1_HUMAN) | 66.37 | 13 | 129 | 25.48 | 8.41 | 2.13 | 4.24E−07 |
| Glutathione S-transferase Mu 1 (GSTM1_HUMAN) | 48.17 | 3 | 24 | 25.70 | 6.70 | 0.46 | 6.84E−04 | |
| Glutathione S-transferase Mu 2 (GSTM2_HUMAN) | 61.47 | 8 | 31 | 25.73 | 6.37 | 0.49 | 4.40E−03 | |
| Glutathione S-transferase Mu 3 (GSTM3_HUMAN) | 52.44 | 4 | 43 | 26.54 | 5.54 | 0.37 | 5.16E−04 | |
| Glutathione S-transferase Mu 4 (A0A0A0MR85_HUMAN) | 26.61 | 1 | 14 | 25.55 | 5.90 | 0.59 | 8.21E−03 | |
| Glutathione S-transferase Mu 5 (GSTM5_HUMAN) | 36.7 | 2 | 25 | 25.66 | 7.39 | 0.59 | 4.01E−04 | |
| Glutathione S-transferase pi (fragment) (C7DJS2_HUMAN) | 42.38 | 1 | 14 | 16.66 | 5.10 | 2.02 | 3.78E−02 | |
| Maleylacetoacetate isomerase (MAAI_HUMAN) | 26.85 | 1 | 7 | 24.20 | 8.54 | 1.59 | 3.61E−03 | |
| Maleylacetoacetate isomerase (G3V5T0_HUMAN) | 28.71 | 1 | 7 | 22.60 | 7.69 | 2.07 | 8.20E−04 |