Table 1 Expression of matrisome genes in RPMI 8226 cells after N1 and N2 knockdown.
Division | Category | Gene symbol | Gene name | shRNA#1 [log2FC] | shRNA#2 [log2FC] | ||
|---|---|---|---|---|---|---|---|
N1 knockdown | Genes up | Cor matrisome | ECM glycoproteins | IGFBP2 | Insulin-like growth factor binding protein 2, 36 kDa | 0.705 | 0.741 |
ZP1 | Zona pellucida glycoprotein 1 (sperm receptor) | 0.543 | 1.017 | ||||
Matrisome-associated | ECM-affiliated proteins | LEFTY2 | Left-right determination factor 2 | 0.97 | 1.853 | ||
PDGFB | Platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) | 0.581 | 0.786 | ||||
Genes down | Core matrisome | ECM glycoproteins | IGFBP4 | Insulin-like growth factor binding protein 4 | −1.364 | −2.331 | |
SPP1 | Secreted phosphoprotein 1 | −1.630 | −1.471 | ||||
Proteoglycans | HAPLN3 | Hyaluronan and proteoglycan link protein 3 | −0.645 | −1.355 | |||
Matrisome-associated | ECM-affiliated proteins | MUC1 | Mucin 1, cell surface associated | −0.563 | −0.524 | ||
ECM regulators | MMP13 | Matrix metallopeptidase 13 (collagenase 3) | −0.824 | −4.088 | |||
Secreted factors | CCL2 | Chemokine (C-C motif) ligand 2 | −1.423 | −1.950 | |||
CCL3 | Chemokine (C-C motif) ligand 3 | −0.837 | −1.722 | ||||
CCL5 | Chemokine (C-C motif) ligand 5 | −0.960 | −2.597 | ||||
CCL8 | Chemokine (C-C motif) ligand 8 | −2.274 | −3.680 | ||||
CXCL10 | Chemokine (C-X-C motif) ligand 10 | −1.005 | −4.661 | ||||
CXCL9 | Chemokine (C-X-C motif) ligand 9 | −1.969 | −4.213 | ||||
IGF1 | Insulin-like growth factor 1 (somatomedin C) | −0.500 | −1.089 | ||||
IL10 | Interleukin 10 | −1.451 | −1.910 | ||||
TNFSF10 | Tumor necrosis factor (ligand) superfamily, member 10 | −0.697 | −3.138 | ||||
TNFSF13B | Tumor necrosis factor (ligand) superfamily, member 13b | −1.563 | −3.153 | ||||
WNT5A | Wingless-type MMTV integration site family, member 5A | −0.688 | −0.553 | ||||
N2 knockdown | Genes up | Core matrisome | ECM glycoproteins | EMID1 | EMI domain containing 1 | 1.199 | 0.995 |
TGFBI | Transforming growth factor, beta-induced, 68 kDa | 0.729 | 0.851 | ||||
THBS2 | Thrombospondin 2 | 0.694 | 0.795 | ||||
ZP1 | Zona pellucida glycoprotein 1 (sperm receptor) | 0.858 | 0.694 | ||||
Matrisome-associated | ECM-affiliated proteins | C1QA | Complement component 1, q subcomponent, A chain | 0.577 | 0.770 | ||
ECM regulators | CTSF | Cathepsin F | 0.940 | 0.605 | |||
TMPRSS15 | Protease, serine, 7 (enterokinase) | 1.646 | 0.742 | ||||
SERPINE1 | Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 | 0.559 | 2.133 | ||||
Secreted factors | S100A9 | S100 calcium binding protein A9 | 1.065 | 0.958 | |||
TNFSF4 | Tumor necrosis factor (ligand) superfamily, member 4 | 0.621 | 0.632 | ||||
WNT5B | Wingless-type MMTV integration site family, member 5B | 0.717 | 0.529 | ||||
Genes down | Core matrisome | ECM glycoproteins | AGRN | Agrin | −1.081 | −0.714 | |
IGFBP3 | Insulin-like growth factor binding protein 3 | −0.725 | −0.776 | ||||
IGFBP4 | Insulin-like growth factor binding protein 4 | −2.309 | −2.075 | ||||
LRG1 | Leucine-rich alpha-2-glycoprotein 1 | −0.948 | −0.621 | ||||
NTNG2 | Netrin G2 | −0.774 | −0.768 | ||||
Collagens | COL16A1 | Collagen, type XVI, alpha 1 | −0.850 | −0.507 | |||
Proteoglycans | HAPLN3 | Hyaluronan and proteoglycan link protein 3 | −1.399 | −0.67 | |||
Matrisome-associated | ECM-affiliated proteins | LGALS9 | Lectin, galactoside-binding, soluble, 9 | −2.045 | −0.932 | ||
SEMA6D | Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D | −0.557 | −0.704 | ||||
ECM regulators | HPSE | Heparanase | −0.934 | −1.146 | |||
KY | Kyphoscoliosis peptidase | −0.919 | −0.875 | ||||
MMP13 | Matrix metallopeptidase 13 (collagenase 3) | −4.951 | −2.381 | ||||
PLOD2 | pProcollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 | −0.978 | −0.770 | ||||
SERPING1 | Serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 | −2.603 | −2.389 | ||||
Secreted factors | ANGPTL6 | Angiopoietin-like 6 | −1.012 | −0.590 | |||
CCL2 | Chemokine (C-C motif) ligand 2 | −2.484 | −1.191 | ||||
CCL3 | Chemokine (C-C motif) ligand 3 | −2.761 | −1.950 | ||||
CCL3L3 | Chemokine (C-C motif) ligand 3-like 3 | −1.719 | −1.452 | ||||
CCL4 | Chemokine (C-C motif) ligand 4 | −1.092 | −0.677 | ||||
CCL5 | Chemokine (C-C motif) ligand 5 | −2.895 | −1.974 | ||||
CCL8 | Chemokine (C-C motif) ligand 8 | −3.697 | −3.540 | ||||
CXCL10 | Chemokine (C-X-C motif) ligand 10 | −5.609 | −2.752 | ||||
CXCL11 | Chemokine (C-X-C motif) ligand 11 | −2.226 | −1.982 | ||||
CXCL12 | Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) | −1.227 | −0.556 | ||||
CXCL9 | Chemokine (C-X-C motif) ligand 9 | −4.870 | −3.239 | ||||
CXCL8 | Interleukin 8 | −0.812 | −0.591 | ||||
IL15 | Interleukin 15 | −1.021 | −0.743 | ||||
IL1RN | Interleukin 1 receptor antagonist | −1.721 | −1.592 | ||||
IL23A | Interleukin 23, alpha subunit p19 | −0.827 | −0.527 | ||||
MDK | Midkine (neurite growth-promoting factor 2) | −0.635 | −0.750 | ||||
S100A6 | S100 calcium-binding protein A6 | −0.713 | −0.577 | ||||
TNFSF10 | Tumor necrosis factor (ligand) superfamily, member 10 | −3.623 | −2.403 | ||||
TNFSF13B | Tumor necrosis factor (ligand) superfamily, member 13b | −3.128 | −2.314 |
