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

Yoon, Cheol Soo; Kim, Min Keun; Kim, Yeon Sook; Lee, Suk Keun

doi:10.1186/s40902-018-0183-z

Maxillofacial Plastic and Reconstructive Surgery

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^*, PCNA^a, CDK4^a, PLK4^a, lamin A/C, MPM2^a, cyclin D2, p14, p16^a, p21^a, p27^a
cMyc/MAX/MAD network proteins	3	cMyc^a, MAX^a, MAD^a
p53/Rb/E2F signaling proteins	5 (1)	p53, Rb-1^#, E2F-1^a, MDM2^a, (CDK4)
Wnt/β-catenin signaling proteins	5	Wnt1^a, β-catenin^a, APC^a, snail^a, TCF-1^a
Epigenetic modification proteins	6	DMAP1^a, histone H1^a, KDM4D^$, HDAC-10^$, MBD4^a, DNMT1^a
Protein translation proteins	5	DOHH^a, DHS^a, elF5A-1^$, elF5A-2^$, eIF2AK3^a
Growth factor proteins	16	FGF-1^a, FGF-2^a, HGF-1^a, TGF-β1^#, TGF-β2, SMAD4^a, IGF-1^a, IGFIIR^a, GH^a, GHRH^a, HER1^a, HER2^a, Erβ^a, insulin^@, Met^a, CTGF^a
RAS signaling proteins	12	NRAS^$, KRAS^$, STAT3^a, SOS-1^a, SOS-2^a, RAF-B^a, JNK-1^a, ERK1^a, p-ERK^$, MEKK^a, pAKT1/2/3, PI3K^a
NFkB signaling proteins	12 (2)	NFkB^a, IKK^a, GADD45^a, GADD153, MDR^a, mTOR^@, p38^a, p-p38^a, AMPK, PGC-1α, (ERK1^a, p-ERK^a)
Cellular stress and adaptation proteins	16 (8)	LC3^a, PLC-β2^a, PKC^a, p-PKC^a, AKAP^a, NFAT5^a, leptin^a, HXK II^a, (pAKT1/2/3^a, p38^a, GADD45^a, PI3K^a, MDM2^a, mTOR^a, ERK-1^a, MDR^a)
Inflammatory proteins upregulated	13 (2)	IL-8, IL-12^a, CD31^a, COX1, α1-AT, LL-37, hepcidin^a, (TGF- β1^#, TGF- β2), MMP-1^a, MMP-3^a, MMP-9^a, MMP-10^a
Inflammation proteins downregulated	17	TNFα^@, IL-1^a, IL-6^a, IL-10^a, IL-28^a, M-CSF^a, lysozyme^a, COX-2^a, CD56^a, CD68^a, CD99^a, cathepsin C^a, cathepsin G^a, CRP-1^a, lactoferrin^a, MMP-2^a, MMP-12^a
Cellular differentiation proteins	11	TGase-2^$, p63^$, caveolin^a, Jagged2^a, Notch 1^a, GLI-1^a, Muc1^a, Muc4^a, AP-1^a, SP-1^a, SP-3^a
Antioxidant and protection-related	11 (2)	HO-1^a, SOD-1^a, GST-1^a, NOS-1^$, LC3^a, HSP-27^a, HSP-70^a, HSP-90^a, (leptin^a, hepcidin), NRF2^a
p53-mediated apoptosis proteins	13 (2)	BCL2^a, BAX^a, BAD^a, BAK^a, BID^a, AIF^a, APAF-1^a, caspase 9^a, c-caspase 9^a, PARP^a, c-PARP^a(p53^a, MDM2^a)
FAS-mediated apoptosis proteins	9 (1)	FASL^a, FAS^a, FADD^a, FLIP^a, caspase 8^a, caspase 3^a, c-caspase 3^a, (BID)
Oncogenic proteins	12 (4)	PTEN^&, DMBT-1^a, CEA^a, 14–3-3^a, survivin^@, YAP^a 1, TERT^a, (pAKT1/2/3^a, MBD4^a, Muc1^a, Muc4^a), ATM^a
Angiogenesis-related proteins	17 (4)	HIF^&, VEGF-A^a, VEGF-C^a, angiogenin^$, LYVE-1^a, CMG2^$, vWF^$, FLT-4^$, ET-1^a, PAI-1^a, plasminogen, PDGF-A^a, VCAM^a, (COX-1^a, leptin^a, CD31, FGF-2^a)
Control housekeeping proteins	3	α-tubulin^a, β-actin^a, GAPDH^a
Total	223 (26)	tTotal 197 antibodies

The number inside the parenthesis represents the antibodies overlapped
^aSanta Cruz Biotechnology, USA
^#DAKO, Denmark
^$Neomarkers, CA, USA
^@ZYMED, CA, USA
^&Abcam, Cambridge, UK
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

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