Table 1. Stromal cell-enriched proteins that are up- or downregulated in colon cancer.
| Accession | Name | Unused Scorea | %Cov (95)b | Peptides (95%)c | Average fold changed | In colorectal cancere | ||
|---|---|---|---|---|---|---|---|---|
| Up | Down | Total | ||||||
| P02462 | COL4A1 (Collagen alpha-1(IV) chain) | 17.7 | 10.5 | 13 | 10.1 | 21 | – | 26 |
| P05997 | COL5A2 (Collagen alpha-2(V) chain) | 50.2 | 29.9 | 37 | 30.5 | 19 | – | 23 |
| P07942 | LAMB1 (Laminin subunit beta-1) | 81.8 | 28.3 | 50 | 22.2 | 16 | – | 27 |
| P12111 | COL6A3 (Collagen alpha-3(VI) chain) | 188.9 | 40.0 | 116 | 26.9 | 19 | – | 26 |
| P35442 | THBS2 (Thrombospondin-2) | 4.4 | 5.5 | 6 | 8.7 | 19 | – | 26 |
| Q02809 | PLOD1 (Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1) | 37.1 | 37.5 | 23 | 3.3 | 19 | 1 | 24 |
| Q15084 | PDIA6 (Protein disulfide-isomerase A6) | 16.1 | 26.8 | 9 | 4.4 | 20 | – | 23 |
| Q16610 | ECM1 (Extracellular matrix protein 1) | 24.6 | 30.7 | 17 | 10.7 | 17 | – | 25 |
| Q96AY3 | FKBP10 (Peptidyl-prolyl cis-trans isomerase FKBP10) | 24.3 | 31.3 | 14 | 12.1 | 15 | – | 24 |
| Q96CG8 | CTHRC1 (Collagen triple helix repeat-containing protein 1) | 4.5 | 11.5 | 3 | 6.3 | 20 | 1 | 23 |
| Q99715 | COL12A1 (Collagen alpha-1(XII) chain) | 142.8 | 35.1 | 85 | 17.0 | 22 | 1 | 23 |
| Q9BUD6 | SPON2 (Spondin-2) | 26.5 | 58.3 | 17 | 9.8 | 20 | – | 24 |
| Q9Y240 | CLEC11A (C-type lectin domain family 11 member A) | 14.6 | 26.0 | 7 | 4.3 | 15 | – | 23 |
| P00749 | PLAU (Urokinase-type plasminogen activator) | 12.8 | 25.1 | 10 | 13.9 | 23 | – | 25 |
| P01033 | TIMP1 (Metalloproteinase inhibitor 1) | 55.9 | 72.0 | 80 | 6.0 | 24 | – | 25 |
| P08254 | MMP3 (Stromelysin-1) | 28.7 | 29.1 | 16 | 8.2 | 24 | – | 24 |
| P67936 | TPM4 (Tropomyosin alpha-4 chain) | 12.2 | 31.0 | 12 | 11.1 | 23 | – | 27 |
| Q13162 | PRDX4 (Peroxiredoxin-4) | 4.0 | 13.3 | 4 | 2.2 | 24 | – | 26 |
| Q15121 | PEA15 (Astrocytic phosphoprotein PEA-15) | 10.0 | 62.3 | 5 | 4.5 | 23 | 1 | 27 |
| Q15582 | TGFBI (Transforming growth factor-beta-induced protein ig-h3) | 51.1 | 51.4 | 52 | 13.0 | 24 | – | 26 |
| O00469 | PLOD2 (Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2) | 16.3 | 20.4 | 13 | 6.2 | – | 15 | 25 |
| P01023 | A2M (Alpha-2-macroglobulin) | 35.5 | 21.4 | 25 | 3.1 | 1 | 26 | 27 |
| P55083 | MFAP4 (Microfibril-associated glycoprotein 4)FF | 6.0 | 13.7 | 3 | 5.1 | – | 18 | 25 |
| Q10588 | BST1 (ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2) | 3.9 | 7.5 | 2 | 8.7 | – | 20 | 26 |
| Q14019 | COTL1 (Coactosin-like protein) | 9.1 | 26.8 | 6 | 4.0 | 1 | 15 | 24 |
| Q14315 | FLNC (Filamin-C) | 79.4 | 24.5 | 49 | 18.1 | 1 | 15 | 24 |
| Q16394 | EXT1 (Exostosin-1) | 14.6 | 14.3 | 10 | 4.7 | – | 23 | 25 |
| Q9UBX5 | FBLN5 (Fibulin-5) | 13.0 | 18.8 | 7 | 8.9 | 1 | 16 | 24 |
Unused (ProtScore) is calculated by ProteinPilot software from the peptide confidence for peptides from spectra that are not already completely “used” by higher scoring winning proteins. This is the maximal value in all three LC-MS runs.
% Cov (95) indicates the percentage of matching amino acids from identified peptides having confidence > = 95% divided by the total number of amino acids in the sequence. This is the maximal value in all three LC-MS runs.
Peptides (95%) is the number of distinct peptides having at least 95% confidence calculated by ProteinPilot. This is the maximal value in all three LC-MS runs.
The average fold change indicates the comparison between the fibroblasts and the epithelial cancer cells.
The mRNA expression of the identified protein is analyzed using Oncomine database (https://www.oncomine.org). The numbers indicate the analysis numbers that exceeding the threshold p value 0.05. The fold change and gene rank are set as “all” and the data type is restricted to mRNA.