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Table 2 Antibodies used in the study

From: In vivo protein expression changes in mouse livers treated with dialyzed coffee extract as determined by IP-HPLC

Signaling proteins No. Antibodies
Proliferation-related proteins 11 Ki-67*, PCNAa, CDK4a, PLK4a, lamin A/C, MPM2a, cyclin D2, p14, p16a, p21a, p27a
cMyc/MAX/MAD network proteins 3 cMyca, MAXa, MADa
p53/Rb/E2F signaling proteins 5 (1) p53, Rb-1#, E2F-1a, MDM2a, (CDK4)
Wnt/β-catenin signaling proteins 5 Wnt1a, β-catenina, APCa, snaila, TCF-1a
Epigenetic modification proteins 6 DMAP1a, histone H1a, KDM4D$, HDAC-10$, MBD4a, DNMT1a
Protein translation proteins 5 DOHHa, DHSa, elF5A-1$, elF5A-2$, eIF2AK3a
Growth factor proteins 16 FGF-1a, FGF-2a, HGF-1a, TGF-β1#, TGF-β2, SMAD4a, IGF-1a, IGFIIRa, GHa, GHRHa, HER1a, HER2a, Erβa, insulin@, Meta, CTGFa
RAS signaling proteins 12 NRAS$, KRAS$, STAT3a, SOS-1a, SOS-2a, RAF-Ba, JNK-1a, ERK1a, p-ERK$, MEKKa, pAKT1/2/3, PI3Ka
NFkB signaling proteins 12 (2) NFkBa, IKKa, GADD45a, GADD153, MDRa, mTOR@, p38a, p-p38a, AMPK, PGC-1α, (ERK1a, p-ERKa)
Cellular stress and adaptation proteins 16 (8) LC3a, PLC-β2a, PKCa, p-PKCa, AKAPa, NFAT5a, leptina, HXK IIa, (pAKT1/2/3a, p38a, GADD45a, PI3Ka, MDM2a, mTORa, ERK-1a, MDRa)
Inflammatory proteins upregulated 13 (2) IL-8, IL-12a, CD31a, COX1, α1-AT, LL-37, hepcidina, (TGF- β1#, TGF- β2), MMP-1a, MMP-3a, MMP-9a, MMP-10a
Inflammation proteins downregulated 17 TNFα@, IL-1a, IL-6a, IL-10a, IL-28a, M-CSFa, lysozymea, COX-2a, CD56a, CD68a, CD99a, cathepsin Ca, cathepsin Ga, CRP-1a, lactoferrina, MMP-2a, MMP-12a
Cellular differentiation proteins 11 TGase-2$, p63$, caveolina, Jagged2a, Notch 1a, GLI-1a, Muc1a, Muc4a, AP-1a, SP-1a, SP-3a
Antioxidant and protection-related 11 (2) HO-1a, SOD-1a, GST-1a, NOS-1$, LC3a, HSP-27a, HSP-70a, HSP-90a, (leptina, hepcidin), NRF2a
p53-mediated apoptosis proteins 13 (2) BCL2a, BAXa, BADa, BAKa, BIDa, AIFa, APAF-1a, caspase 9a, c-caspase 9a, PARPa, c-PARPa(p53a, MDM2a)
FAS-mediated apoptosis proteins 9 (1) FASLa, FASa, FADDa, FLIPa, caspase 8a, caspase 3a, c-caspase 3a, (BID)
Oncogenic proteins 12 (4) PTEN&, DMBT-1a, CEAa, 14–3-3a, survivin@, YAPa 1, TERTa, (pAKT1/2/3a, MBD4a, Muc1a, Muc4a), ATMa
Angiogenesis-related proteins 17 (4) HIF&, VEGF-Aa, VEGF-Ca, angiogenin$, LYVE-1a, CMG2$, vWF$, FLT-4$, ET-1a, PAI-1a, plasminogen, PDGF-Aa, VCAMa, (COX-1a, leptina, CD31, FGF-2a)
Control housekeeping proteins 3 α-tubulina, β-actina, GAPDHa
Total 223 (26) tTotal 197 antibodies
  1. The number inside the parenthesis represents the antibodies overlapped
  2. aSanta Cruz Biotechnology, USA
  3. #DAKO, Denmark
  4. $Neomarkers, CA, USA
  5. @ZYMED, CA, USA
  6. &Abcam, Cambridge, UK
  7. Abbreviations: α1-AT α-1 antitrypsin; AMPK AMP-activated protein kinase; p-AKT1/2/3 phosphorylated (p-Akt, Thr 308); APAF-1 apoptotic protease-activating factor 1; AP-1 activating protein-1; BAD BCL2 associated death promoter; BAK BCL2 antagonist/killer; BAX BCL2-associated X; BCL-2 B-cell leukemia/lymphoma-2; BID BH3 interacting-domain death agonist; c-caspase 3 cleaved-caspase 3, caveolin; CD31/56/68/99 cluster of differentiation 31/56/68/99; CDK4 cyclin-dependent kinase 4; CEA carcinoembryonic antigen; CMG2 capillary morphogenesis protein 2; COX-1 cyclooxygenase-2; COX-2 cyclooxygenase-2; c-PARP cleaved-PARP (poly-ADP ribose polymerase); CTGF connective tissue growth factor, cyclin D2; DMAP1 DNA methyltransferase 1-associated protein; DMBT1 deleted in malignant brain tumors 1; DOHH deoxyhypusine hydroxylase; DHS deoxyhypusine synthase; E2F-1 transcription factor; eIF2AK3 (PERK) eukaryotic translation initiation factor 2 (protein kinase R (PKR)-like endoplasmic reticulum kinase); elF5A-1 eukaryotic translation initiation factor 5A-1; elF5A-2 eukaryotic translation initiation factor 5A-2; ERβ estrogen receptor beta; ERK extracellular signal-regulated protein kinases; ET-1 endothelin-1; FAS; CD95/Apo1; FASL FAS ligand; FADD FAS associated via death domain; 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; GST-1 glutathione S-transferase-1; HDAC-10 hepcidin; HIF hypoxia inducible factor-1α; HO-1 heme oxygenase 1; HER2 human epidermal growth factor receptor 2; HGF hepatocyte growth factor; HSP-27/70/90 heat shock protein-27/70/90; HXK II hexokinase II; IKK IkappaB kinase, IGF-1, IGFIIR; IL-1/6/8/12/28 interleukin-1/6/8/12/28, Jagged2; JNK-1 Jun N-terminal protein kinase; KRAS V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog; LC3 microtubule-associated protein 1A/1B-light chain 3, leptin; LYVE-1 lymphatic vessel endothelial hyaluronan receptor 1, MAX Myc-associated factor X; MBD4 methyl-CpG-binding domain protein 4; M-CSF macrophage colony-stimulating factor; MEKK MEK kinase; MDM2 mouse double minute 2 homolog; MDR multiple drug resistance; MPM2 mitotic protein monoclonal 2; mTOR mammalian target of rapamycin; cMyc V-myc myelocytomatosis viral oncogene homolog; NOS-1 nitric oxide synthase 1; NRAS neuroblastoma RAS viral oncogene homolog, Notch 1, p16, p21, p27, p38, p53, p63, PAI plasminogen activator inhibitor-1; PARP poly-ADP ribose polymerase; PCNA proliferating cell nuclear antigen, PDGF-A platelet-derived growth factor-A; PLC-β2 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterse β-2; PI3K phosphatidylinositol-3-kinases; PLK4 polo-like kinase 4 or serine/threonine-protein kinase; PKC protein kinase C, p-p38 phosphor-p38; PTEN phosphatase and tensin homolog; Rb-1 retinoblastoma-1; SMAD4 mothers against decapentaplegic; drosophila homolog 4; SOD-1 superoxide dismutase-1; SP-1 specificity protein 1; STAT3 signal transducer and activator of transcription-3; TGF-β1 transforming growth factor-β1; TERT human telomerase reverse transcriptase; TNF-α tumor necrosis factor-α, β-actin, 14-3-3; VEGF vascular endothelial growth factor; VCAM vascular cell adhesion, vWF Von Willebrand factor; YAP 1 yes-associated protein