Table 1. Antibodies used in the study.
| Proteins | No. | Antibodies |
|---|---|---|
| Proliferation-related proteins | 11 | Ki-67*, PCNA*, CDK4*, MPM2*, PLK4*, cyclin D2, p14*, p15/16*, p21*, p27*, lamin A/C* |
| cMyc/MAX/MAD network | 4 (1) | cMyc*, MAX*, MAD-1*, (p27) |
| p53/Rb/E2F signaling | 4 (1) | p53, Rb-1#, E2F-1*, (CDK4) |
| Wnt/β-catenin signaling | 7 | Wnt1*, β-catenin*, APC*, snail*, TCF-1*, E-cadherin*, VE-cadherin& |
| Epigenetic modification | 7 | histone H1*, DMAP1*, KDM4D$, HDAC10$, MBD4*, DNMT1*, PCAF* |
| Protein translation | 7 | DOHH!, DHS!, elF5A-1!, eIF2AK3 (PERK)*, p-eIF2AK3 (Thr981)*, eIF2α^, p-eIF2α (Ser51)^ |
| Growth factor | 20 | TGF-β1#, TGF-β2*, TGF-β3*, SMAD2/3, SMAD4*, p-SMAD4, HGFα*, Met*, FGF-1*, FGF-2*, FGF-7*, GH*, GHRH*, IGF-1*, IGFIIR*, PDGF-A*, CTGF*, HER1*, HER2*, ERβ*, |
| RAS signaling proteins | 21 | NRAS$, KRAS$, HRAS, STAT3*, PI3K, RAF-B*, JNK-1*, p-JNK-1, JAK2$, ERK-1*, p-ERK-1 (T202, Y204)$, Rab 1*, p38, p-p38 (Thr180, Tyr182), pAKT1/2/3 (Thr308), AKAP, mTOR@, PTEN, PKC*, p-PKC1α (Thr514)@, SOS-1/2* |
| NFkB signaling proteins | 19 (11) | NFkB*, IKK*, (p38*, p-p38*), GADD45*, GADD153* (CHOP)*, (mTOR@, PKC*, p-PKC1α@), NRF-2*, (JAK2, ERK-1*, p-ERK-1$), PGC-1α, (pAKT1/2/3, AKAP, SRC-1*), MDR, AMPKα@, |
| Upregulated inflammatory proteins | 20 | IL-1*, IL-10*, IL-12*, cathepsin K*, lysozyme*, granzyme B, lactoferrin, M-CSF, β-defensin-1, β-defensin-2, β-defensin-3, CD28, Pdcd-1/1 (CD279), PECAM-1 (CD31)*, HCAM (CD44)*, ICAM-1 (CD54)*, versican*, COX1*, COX2*, kininogen* |
| Downregulated inflammatory proteins | 25 | TNFα@, IL-6*, IL-8, IL-28*, LTA4H&, CXCR4*, MMP-1, -2, -3$, -9$, -10, -12$, cathepsin C*, cathepsin G*, MCP-1, LL-37, α1- antitrypsin &, CD20, CD34, CD68, CD80 (B7-1), CD99 (MIC2), NCAM (CD56), VCAM-1 (CD106), CTLA4*, TLR3* |
| p53-mediated apoptosis | 15 (1) | (p53*), MDM2*, BAD*, BID*, BAK*, NOXA*, PUMA*, BAX*, BCL2*, APAF-1*, caspase 9*, c-caspase 9*, PARP-1*, c-PARP-1*, AIF* |
| FAS-mediated apoptosis | 9 (1) | FASL*, FAS*, FADD*, FLIP*, (BID*), c-caspase 8*, c-caspase 10*, caspase 3*, c-caspase 3* |
| Protection- and survival-related proteins | 20 (4) | PKC, p-PKC1α, (pAKT1/2/3), HSP-27*, HSP-70*, HSP-90*, LC3, (AMPKα, PGC-1α), TERT*, SP-1@, SP-3@, NOS-1$, leptin, PLC-β2, HO-1*, SOD-1*, GSTO1*, SVCT2&, (NRF2) |
| Differentiation-related proteins | 18 (1) | α-actin*, p63$, vimentin*, TGase-2, -4, caveolin-1*, GLI1, Jagged1*, Notch1, S-100*, AP1M1*, CaM*, cystatin A*, SHH*, FAK*, (PLC-β2), integrin α5*, CRIP-1* |
| Endoplasmic reticulum stress-related proteins | 11 (10) | (HSP-27, HSP-70, eIF2AK3* (PERK), p-EIF2AK3 (p-PERK)), ATF4*, ATF6*, (GADD153 (CHOP)*, LC3, AIF, AP1M1, endothelin-1, PGC-1α) |
| Oncogenesis-related proteins | 17 (2) | PTEN&, BRCA1&, BRCA2&, NF-1*, (MBD4), ATM*, PTCH-1, maspin*, DMBT1*, PIM-1*, CEA$, 14-3-3*, survivin@, mucin 1*, mucin 4*, YAP*, (CRIP1) |
| Angiogenesis-related proteins | 23 (9) | HIF-1α&, angiogenin$, VEGF-A*, VEGF-C*, VEGFR2*, p-VEGFR2 (Y951), vWF$, CMG2$, FLT-4$, LYVE-1*, (FGF-2, PDGF-A, MMP-2, MMP-10), endothelin-1*, plasminogen*, PAI-1*, fibrinogen*, (kininogen-1, HCAM*, VCAM-1*, ICAM-1*, PECAM-1*) |
| Osteogenesis-related proteins | 17 (5) | BMP-2*, BMP-3*, BMP-4*, OPG*, RANKL*, osteocalcin*, osteopontin*, osteonectin*, RUNX2*, osterix*, (TGF-β1), ALP*, (cathepsin K*, HSP-90*, versican*), aggrecan*, (CTGF*) |
| Control housekeeping proteins | 3 | α-tubulin*, β-actin*, GAPDH* |
| Total | 278 (46) |
* Santa Cruz Biotechnology, USA
# DAKO, Denmark
$ Neomarkers, CA, USA
@ ZYMED, CA, USA
&Abcam, Cambridge, UK
^Cell signaling technology, USA
! kindly donated from Dr. M. H. Park in NIH, USA [38], the number of antibodies overlapped; ().
Abbreviations: AIF; apoptosis inducing factor, AKAP; A-kinase anchoring proteins, ALP; alkaline phosphatase, AMPK; AMP-activated protein kinase, pAKT; v-akt murine thymoma viral oncogene homolog, p-Akt1/2/3 phosphorylated (p-Akt, Thr 308), APAF-1; apoptotic protease-activating factor 1, APC; adenomatous polyposis coli, ATF4; activating transcription factor 4, ATM; ataxia telangiectasia caused by mutations, BAD; BCL2 associated death promoter, BAK; BCL2 antagonist/killer, BAX; BCL2 associated X, BCL2; B-cell leukemia/lymphoma-2, BID; BH3 interacting-domain death agonist, BMP-2; bone morphogenesis protein 2, BRCA1; breast cancer type 1 susceptibility protein, c-caspase 3; cleaved-caspase 3, CaM; calmodulin, CD3; cluster of differentiation 3, CDK4; cyclin dependent kinase 4, CEA; carcinoembryonic antigen, CHOP (GADD153); C/EBP homologous protein, CMG2: capillary morphogenesis protein 2, COX-1; cyclooxygenase-2, CTGF connective tissue growth factor, CTLA4; cytotoxic T lymphocyte-associated protein-4, CXCR4; C-X-C chemokine receptor type 4, DHS; deoxyhypusine synthase, DMAP1; DNA methyltransferase 1 associated protein, DMBT1; deleted in malignant brain tumors 1, DNMT1; DNA 5-cytosine methyltransferase 1, DOHH; deoxyhypusine hydroxylase, E2F-1; transcription factor, eIF2AK3 (PERK); protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK), elF5A-1; eukaryotic translation initiation factor 5A-1, ERK-1; extracellular signal-regulated protein kinase 1, ERβ; estrogen receptor beta, FADD; FAS associated via death domain, FAK; focal adhesion kinase, FAS; CD95/Apo1, FASL; FAS ligand, FGF-1; fibroblast growth factor-1, FLIP; FLICE-like inhibitory protein, FLT-4; Fms-related tyrosine kinase 4, GADD45; growth arrest and DNA-damage-inducible 45, GAPDH; glyceraldehyde 3-phosphate dehydrogenase, GH; growth hormone, GHRH; growth hormone-releasing hormone, GSTO1; glutathione S-transferase ω 1, HCAM (CD44); homing cell adhesion molecule, HDAC10; histone deacetylase 10, HER1; human epidermal growth factor receptor 1, HGFα; hepatocyte growth factor α, HIF-1α: hypoxia inducible factor-1α, HO-1; heme oxygenase 1, HRAS; GTPase HRas, HSP-70; heat shock protein-70, ICAM-1 (CD54); intercellular adhesion molecule 1, IGF-1; insulin-like growth factor 1, IGFIIR; insulin-like growth factor 2 receptor, IKK; ikappaB kinase, IL-1; interleukin-1, JAK2; Janus kinase 2, JNK-1; Jun N-terminal protein kinase, KDM4D; Lysine-specific demethylase 4D, KRAS; V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, LC3; microtubule-associated protein 1A/1B-light chain 3, LTA4H; leukotriene A4 hydrolase, LYVE-1: lymphatic vessel endothelial hyaluronan receptor 1, MAD-1; mitotic arrest deficient 1, MAX; myc-associated factor X, MBD4; methyl-CpG-binding domain protein 4, MCP-1; monocyte chemotactic protein 1, M-CSF; macrophage colony-stimulating factor, MDM2; mouse double minute 2 homolog, MDR; multiple drug resistance, MMP-1; matrix metalloprotease-1, MPM2; mitosis phase promoting factor (MPF) recognized by a mitosis-specific monoclonal antibody, mitotic protein monoclonal 2, mTOR; mammalian target of rapamycin, cMyc; V-myc myelocytomatosis viral oncogene homolog, NFkB; nuclear factor kappa-light-chain-enhancer of activated B cells, NCAM (CD56); neural cell adhesion molecule 1, NF-1; neurofibromin 1, NFkB; nuclear factor kappa-light-chain-enhancer of activated B cells, NOS-1; nitric oxide synthase 1, NOXA; Phorbol-12-myristate-13-acetate-induced protein 1, NRAS; neuroblastoma RAS Viral Oncogene homolog, NRF2; nuclear factor (erythroid-derived)-like 2, OPG; osteoprotegerin, PAI-1; plasminogen activator inhibitor-1, PARP-1; poly-ADP ribose polymerase 1, c-PARP-1; cleaved-PARP-1, PCAF; p300/CBP-associated factor, PCNA; proliferating cell nuclear antigen, Pdcd-1/1 (CD279); programmed cell death protein 1, PDGF-A: platelet-derived growth factor-A, PECAM-1 (CD31); platelet endothelial cell adhesion molecule-1, PERK; protein-like endoplasmic reticulum kinase, PGC-1α; peroxisome proliferator-activated receptor gamma coactivator 1-α, PI3K; phosphatidylinositol-3-kinase, PIM-1; Proto-oncogene serine/threonine-protein kinase 1, PKC; protein kinase C, PLC-β2; 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterse β-2, PLK4; polo like kinase 4 or serine/threonine-protein kinase, PTEN; phosphatase and tensin homolog, PUMA; p53 upregulated modulator of apoptosis, Rab 1; Rab GTPases, RAF-B; v-Raf murine sarcoma viral oncogene homolog B, RANKL; receptor activator of nuclear factor kappa-B ligand, Rb-1; retinoblastoma-1, RUNX2; Runt-related transcription factor-2, SHH; sonic hedgehog, SMAD4; mothers against decapentaplegic, drosophila homolog 4, SOD-1; superoxide dismutase-1, SOS-1; son of sevenless homolog 1, SP-1; specificity protein 1, SRC1; steroid receptor coactivator-1, STAT3; signal transducer and activator of transcription-3, SVCT2; sodium-dependent vitamin C transporter 2, TERT; human telomerase reverse transcriptase, TGase-2; transglutaminase 2, TGF-β1; transforming growth factor-β1, TNFα; tumor necrosis factor-α, VCAM-1; vascular cell adhesion molecule-1, VE-cadherin; vascular endothelial cadherin, VEGF-A vascular endothelial growth factor A, VEGFR2; vascular endothelial growth factor receptor 2, p-VEGFR2; vascular endothelial growth factor receptor 2 (Y951), vWF; von Willebrand factor, Wnt1; proto-oncogene protein Wnt-1, YAP; Yes-associated protein.