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Supplementary Table 3: Genes Only Influenced By

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Supplementary Table 3: Genes only influenced by X10 Illumina ID Gene ID Entrez Gene Name Fold change compared to vehicle 1810058M03RIK -1.104 2210008F06RIK 1.090 2310005E10RIK -1.175 2610016F04RIK 1.081 2610029K11RIK 1.130 381484 Gm5150 predicted gene 5150 -1.230 4833425P12RIK -1.127 4933412E12RIK -1.333 6030458P06RIK -1.131 6430550H21RIK 1.073 6530401D06RIK 1.229 9030607L17RIK -1.122 A330043C08RIK 1.113 A330043L12 1.054 A530092L01RIK -1.069 A630054D14 1.072 A630097D09RIK -1.102 AA409316 FAM83H family with sequence similarity 83, member H 1.142 AAAS AAAS achalasia, adrenocortical insufficiency, alacrimia 1.144 ACADL ACADL acyl-CoA dehydrogenase, long chain -1.135 ACOT1 ACOT1 acyl-CoA thioesterase 1 -1.191 ADAMTSL5 ADAMTSL5 ADAMTS-like 5 1.210 AFG3L2 AFG3L2 AFG3 ATPase family gene 3-like 2 (S. cerevisiae) 1.212 AI256775 RFESD Rieske (Fe-S) domain containing 1.134 Lipo1 (includes AI747699 others) lipase, member O2 -1.083 AKAP8L AKAP8L A kinase (PRKA) anchor protein 8-like -1.263 AKR7A5 -1.225 AMBP AMBP alpha-1-microglobulin/bikunin precursor 1.074 ANAPC2 ANAPC2 anaphase promoting complex subunit 2 -1.134 ANKRD1 ANKRD1 ankyrin repeat domain 1 (cardiac muscle) 1.314 APOA1 APOA1 apolipoprotein A-I -1.086 ARHGAP26 ARHGAP26 Rho GTPase activating protein 26 -1.083 ARL5A ARL5A ADP-ribosylation factor-like 5A -1.212 ARMC3 ARMC3 armadillo repeat containing 3 -1.077 ARPC5 ARPC5 actin related protein 2/3 complex, subunit 5, 16kDa -1.190 activating transcription factor 4 (tax-responsive enhancer element ATF4 ATF4 B67) 1.481 AU014645 NCBP1 nuclear cap binding protein subunit 1, 80kDa 1.158 AV028368 TMEM201 transmembrane protein 201 1.273 BC013529 C6orf72 chromosome 6 open reading frame 72 -1.266 BC018242 LPPR2 lipid phosphate phosphatase-related protein type 2 1.095 BC018507 KIAA0947 KIAA0947 1.100 BC025546 FTSJD1 FtsJ methyltransferase domain containing 1 1.134 BC039210 PIEZO1 piezo-type mechanosensitive ion channel component 1 1.354 BNC1 BNC1 basonuclin 1 1.268 BSN BSN bassoon (presynaptic cytomatrix protein) 1.103 C130035G06RIK 1.105 C130037I06RIK 1.063 C130080K17RIK -1.065 C230098O21RIK -1.116 C3 NAD+ -1.608 CAMSAP1 CAMSAP1 calmodulin regulated spectrin-associated protein 1 1.071 CASP7 CASP7 caspase 7, apoptosis-related cysteine peptidase -1.130 CCDC28B CCDC28B coiled-coil domain containing 28B -1.129 CCDC92 CCDC92 coiled-coil domain containing 92 -1.221 CCL9 -1.381 CCT3 CCT3 chaperonin containing TCP1, subunit 3 (gamma) 1.223 CD274 CD274 CD274 molecule -1.321 CD300A CD300A CD300a molecule -1.077 CDK2AP2 CDK2AP2 cyclin-dependent kinase 2 associated protein 2 -1.152 CDV3 CDV3 CDV3 homolog (mouse) 1.151 CENPA CENPA centromere protein A -1.196 CHAC1 CHAC1 ChaC, cation transport regulator homolog 1 (E. coli) 1.995 CHCHD10 CHCHD10 coiled-coil-helix-coiled-coil-helix domain containing 10 -1.565 CHCHD4 CHCHD4 coiled-coil-helix-coiled-coil-helix domain containing 4 1.281 CIRH1A CIRH1A cirrhosis, autosomal recessive 1A (cirhin) 1.288 CLTA CLTA clathrin, light chain A -1.250 CNR2 CNR2 cannabinoid receptor 2 (macrophage) -1.108 COP9 constitutive photomorphogenic homolog subunit 7A COPS7A COPS7A (Arabidopsis) 1.194 CRELD1 CRELD1 cysteine-rich with EGF-like domains 1 -1.147 CTPS CTPS CTP synthase 1.177 CXCL16 CXCL16 chemokine (C-X-C motif) ligand 16 -1.319 CYB561D1 CYB561D1 cytochrome b-561 domain containing 1 -1.073 CYB5B CYB5B cytochrome b5 type B (outer mitochondrial membrane) 1.210 CYP4F13 -1.311 CYTH4 CYTH4 cytohesin 4 -1.207 D0H8S2298E 1.177 D10ERTD610E -1.165 D130007C19RIK -1.095 D7BWG0611E -1.105 D930046M13RIK 1.133 DALRD3 DALRD3 DALR anticodon binding domain containing 3 -1.212 DCLK2 DCLK2 doublecortin-like kinase 2 1.122 DCN1, defective in cullin neddylation 1, domain containing 3 (S. DCUN1D3 DCUN1D3 cerevisiae) 1.081 DENND4B DENND4B DENN/MADD domain containing 4B 1.135 DHX58 DHX58 DEXH (Asp-Glu-X-His) box polypeptide 58 -1.239 DKK3 DKK3 dickkopf 3 homolog (Xenopus laevis) -1.280 DMAP1 DMAP1 DNA methyltransferase 1 associated protein 1 -1.259 DTX3L DTX3L deltex 3-like (Drosophila) -1.230 DYNC1LI2 DYNC1LI2 dynein, cytoplasmic 1, light intermediate chain 2 1.239 E030010A14RIK -1.106 E030030K01RIK 1.134 E530018B05RIK -1.057 EARS2 EARS2 glutamyl-tRNA synthetase 2, mitochondrial (putative) 1.158 EEF1E1 EEF1E1 eukaryotic translation elongation factor 1 epsilon 1 1.185 EEF1G EEF1G eukaryotic translation elongation factor 1 gamma 1.232 EHHADH EHHADH enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase -1.112 EIF4E EIF4E eukaryotic translation initiation factor 4E 1.118 ENPP1 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 -1.120 ETHE1 ETHE1 ethylmalonic encephalopathy 1 -1.207 EXT1 EXT1 exostosin 1 1.300 FAHD2A FAHD2A fumarylacetoacetate hydrolase domain containing 2A -1.079 FBXW17 -1.157 FBXW5 FBXW5 F-box and WD repeat domain containing 5 -1.176 FKBP1B FKBP1B FK506 binding protein 1B, 12.6 kDa -1.158 FAD1 flavin adenine dinucleotide synthetase homolog (S. FLAD1 FLAD1 cerevisiae) -1.133 FNBP1 FNBP1 formin binding protein 1 -1.181 GAB3 GAB3 GRB2-associated binding protein 3 -1.075 GBP3 GBP3 guanylate binding protein 3 -1.328 GBP6 GBP6 guanylate binding protein family, member 6 -1.134 GCK GCK glucokinase (hexokinase 4) 1.116 GLUD1 GLUD1 glutamate dehydrogenase 1 -1.240 GM528 -1.070 GM684 1.083 GMDS GMDS GDP-mannose 4,6-dehydratase -1.220 GNL2 GNL2 guanine nucleotide binding protein-like 2 (nucleolar) 1.191 GPR120 O3FAR1 omega-3 fatty acid receptor 1 -1.128 GPS2 GPS2 G protein pathway suppressor 2 -1.145 GPX1 (includes GPX1 EG:14775) glutathione peroxidase 1 -1.244 GRP1 (general receptor for phosphoinositides 1)-associated scaffold GRASP GRASP protein -1.199 GSPT1 GSPT1 G1 to S phase transition 1 1.186 GYS3 1.092 H2-KE6 -1.290 HBEGF HBEGF heparin-binding EGF-like growth factor 1.329 HEATR1 HEATR1 HEAT repeat containing 1 1.151 HES6 HES6 hairy and enhancer of split 6 (Drosophila) -1.218 HHAT HHAT hedgehog acyltransferase 1.162 HIST2H2BE (includes HIST1H2BF others) histone cluster 2, H2be -1.403 HIST1H2BH/ HIST1H2BH HIST1H2BO histone cluster 1, H2bh -1.486 HNRPA1 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 1.157 HOXA4 HOXA4 homeobox A4 1.231 HRMT1L6 PRMT6 protein arginine methyltransferase 6 1.123 HS3ST3B1 HS3ST3B1 heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 1.062 HS6ST1 HS6ST1 heparan sulfate 6-O-sulfotransferase 1 1.276 IDB2 -1.164 IFT88 IFT88 intraflagellar transport 88 homolog (Chlamydomonas) -1.193 IGTP -1.450 IIGP2 -1.582 IL11 IL11 interleukin 11 1.136 INPP5K INPP5K inositol polyphosphate-5-phosphatase K -1.189 IPPK IPPK inositol 1,3,4,5,6-pentakisphosphate 2-kinase 1.132 IQCE IQCE IQ motif containing E -1.226 IRF1 (includes IRF1 EG:16362) interferon regulatory factor 1 -1.195 IRF7 IRF7 interferon regulatory factor 7 -1.183 KCNK6 KCNK6 potassium channel, subfamily K, member 6 -1.131 KLC2 KLC2 kinesin light chain 2 1.100 KLF16 KLF16 Kruppel-like factor 16 1.141 KLF6 KLF6 Kruppel-like factor 6 -1.176 KLHDC8B KLHDC8B kelch domain containing 8B 1.062 LARP-PENDING 1.120 LAT2 LAT2 linker for activation of T cells family, member 2 -1.170 LHFPL2 LHFPL2 lipoma HMGIC fusion partner-like 2 1.298 LOC100044298 -1.222 LOC100045708 1.148 LOC100045981 -1.307 LOC100046163 1.116 LOC100046608 -1.087 LOC100047260 1.336 LOC100048554 -2.246 LOC223672 -1.259 LOC230253 1.149 LOC230592 1.164 LOC240672 1.316 LOC277313 -1.125 LOC331336 -1.062 LOC380854 1.075 LOC381466 -1.119 LOC381607 1.091 LOC382866 1.106 LOC383836 1.120 LOC384206 1.179 LOC386553 1.166 LOC666238 1.064 LOC670044 -1.117 LTB4R1 -1.338 LTBP2 LTBP2 latent transforming growth factor beta binding protein 2 1.053 LTC4S LTC4S leukotriene C4 synthase -1.273 LYCAT LCLAT1 lysocardiolipin acyltransferase 1 1.106 MAF1 (includes MAF1 EG:315093) MAF1 homolog (S. cerevisiae) -1.282 MAML1 MAML1 mastermind-like 1 (Drosophila) 1.167 MAN2C1 MAN2C1 mannosidase, alpha, class 2C, member 1 -1.172 MAST3 MAST3 microtubule associated serine/threonine kinase 3 -1.218 MCOLN2 MCOLN2 mucolipin 2 -1.121 MED27 MED27 mediator complex subunit 27 1.179 MFSD1 MFSD1 major facilitator superfamily domain containing 1 -1.276 MKI67IP MKI67IP MKI67 (FHA domain) interacting nucleolar phosphoprotein 1.255 MOCOS MOCOS molybdenum cofactor sulfurase -1.123 MRPL43 MRPL43 mitochondrial ribosomal protein L43 -1.173 MS4A6D -1.343 MSLN MSLN mesothelin 1.194 MYO1G MYO1G myosin IG -1.415 NAPRT1 NAPRT1 nicotinate phosphoribosyltransferase domain containing 1 -1.075 NCF4 NCF4 neutrophil cytosolic factor 4, 40kDa -1.474 NCKAP1L NCKAP1L NCK-associated protein 1-like -1.232 NECAP1 NECAP1 NECAP endocytosis associated 1 1.132 NIT2 NIT2 nitrilase family, member 2 -1.074 NKIRAS2 NKIRAS2 NFKB inhibitor interacting Ras-like 2 1.181 NOD1 NOD1 nucleotide-binding oligomerization domain containing 1 -1.325 NOL1 NOP2 NOP2 nucleolar protein homolog (yeast) 1.259 OASL2 -1.210 OCIAD2 OCIAD2 OCIA domain containing 2 -1.194 OGFRL1 OGFRL1 opioid growth factor receptor-like 1 -1.246 OLFR1390 1.081 OLFR66 1.084 P2RY6 P2RY6 pyrimidinergic receptor P2Y, G-protein coupled, 6 -1.210 PAIP2B PAIP2B poly(A) binding protein interacting protein 2B 1.184 PARP16 PARP16 poly (ADP-ribose) polymerase family, member 16 1.103 PCDHGA4 PCDHGA4 protocadherin gamma subfamily A, 4 1.072 PDE6D PDE6D phosphodiesterase 6D, cGMP-specific, rod, delta -1.303 PICALM PICALM phosphatidylinositol binding clathrin assembly protein 1.212 PIGZ PIGZ phosphatidylinositol glycan anchor biosynthesis, class Z -1.140 PIK3IP1 PIK3IP1 phosphoinositide-3-kinase interacting protein 1 -1.205 PIRA4 -1.140 PODXL PODXL podocalyxin-like 1.180 PPAPDC1 PPAPDC1A phosphatidic acid phosphatase type 2 domain containing 1A 1.261 PPIL1 PPIL1 peptidylprolyl isomerase (cyclophilin)-like 1 1.275 PRDX6-RS2 1.061 PRPF4 PRPF4 PRP4 pre-mRNA processing factor 4 homolog (yeast) 1.144 PTCD2 PTCD2 pentatricopeptide repeat domain 2 1.112 PWWP2B PWWP2B PWWP domain containing 2B 1.093 R3HDM2 R3HDM2 R3H domain containing 2 1.092 RAB32 RAB32 RAB32, member RAS oncogene family -1.214 RAB3D RAB3D RAB3D, member RAS oncogene family -1.183 RASL2-9 -1.078 RBM13 MAK16 MAK16 homolog (S.
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    Hindawi BioMed Research International Volume 2021, Article ID 4873678, 12 pages https://doi.org/10.1155/2021/4873678 Research Article Study of the G Protein Nucleolar 2 Value in Liver Hepatocellular Carcinoma Treatment and Prognosis Yiwei Dong,1 Qianqian Cai,2 Lisheng Fu,1 Haojie Liu,1 Mingzhe Ma,3 and Xingzhong Wu 1 1Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai 200032, China 2Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China 3Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai 200025, China Correspondence should be addressed to Xingzhong Wu; [email protected] Received 10 May 2021; Accepted 29 June 2021; Published 20 July 2021 Academic Editor: Tao Huang Copyright © 2021 Yiwei Dong et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. LIHC (liver hepatocellular carcinoma) mostly occurs in patients with chronic liver disease. It is primarily induced by a vicious cycle of liver injury, inflammation, and regeneration that usually last for decades. The G protein nucleolar 2 (GNL2), as a protein- encoding gene, is also known as NGP1, Nog2, Nug2, Ngp-1, and HUMAUANTIG. Few reports are shown towards the specific biological function of GNL2. Meanwhile, it is still unclear whether it is related to the pathogenesis of carcinoma up to date. Here, our study attempts to validate the role and function of GNL2 in LIHC via multiple databases and functional assays.
  • Epigenetic Mechanisms of Lncrnas Binding to Protein in Carcinogenesis

    Epigenetic Mechanisms of Lncrnas Binding to Protein in Carcinogenesis

    cancers Review Epigenetic Mechanisms of LncRNAs Binding to Protein in Carcinogenesis Tae-Jin Shin, Kang-Hoon Lee and Je-Yoel Cho * Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; [email protected] (T.-J.S.); [email protected] (K.-H.L.) * Correspondence: [email protected]; Tel.: +82-02-800-1268 Received: 21 September 2020; Accepted: 9 October 2020; Published: 11 October 2020 Simple Summary: The functional analysis of lncRNA, which has recently been investigated in various fields of biological research, is critical to understanding the delicate control of cells and the occurrence of diseases. The interaction between proteins and lncRNA, which has been found to be a major mechanism, has been reported to play an important role in cancer development and progress. This review thus organized the lncRNAs and related proteins involved in the cancer process, from carcinogenesis to metastasis and resistance to chemotherapy, to better understand cancer and to further develop new treatments for it. This will provide a new perspective on clinical cancer diagnosis, prognosis, and treatment. Abstract: Epigenetic dysregulation is an important feature for cancer initiation and progression. Long non-coding RNAs (lncRNAs) are transcripts that stably present as RNA forms with no translated protein and have lengths larger than 200 nucleotides. LncRNA can epigenetically regulate either oncogenes or tumor suppressor genes. Nowadays, the combined research of lncRNA plus protein analysis is gaining more attention. LncRNA controls gene expression directly by binding to transcription factors of target genes and indirectly by complexing with other proteins to bind to target proteins and cause protein degradation, reduced protein stability, or interference with the binding of other proteins.
  • Modulating Hallmarks of Cholangiocarcinoma

    Modulating Hallmarks of Cholangiocarcinoma

    University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Fall 12-14-2018 Modulating Hallmarks of Cholangiocarcinoma Cody Wehrkamp University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Molecular Biology Commons Recommended Citation Wehrkamp, Cody, "Modulating Hallmarks of Cholangiocarcinoma" (2018). Theses & Dissertations. 337. https://digitalcommons.unmc.edu/etd/337 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. MODULATING HALLMARKS OF CHOLANGIOCARCINOMA by Cody J. Wehrkamp A DISSERTATION Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biochemistry and Molecular Biology Graduate Program Under the Supervision of Professor Justin L. Mott University of Nebraska Medical Center Omaha, Nebraska November 2018 Supervisory Committee: Kaustubh Datta, Ph.D. Melissa Teoh‐Fitzgerald, Ph.D. Richard G. MacDonald, Ph.D. Acknowledgements This endeavor has led to scientific as well as personal growth for me. I am indebted to many for their knowledge, influence, and support along the way. To my mentor, Dr. Justin L. Mott, you have been an incomparable teacher and invaluable guide. You upheld for me the concept that science is intrepid, even when the experience is trying. Through my training, and now here at the end, I can say that it has been an honor to be your protégé. When you have shaped your future graduates to be and do great, I will be privileged to say that I was your first one.