Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression
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Aamir Shafi | Amjad Ali | Amnah Siddiqa | Zurah Bibi | Shahzina Kanwal | Muhammad Tariq Saeed | I. A. Sheikh | A. Shafi | Amjad Ali | J. Ahmad | Zurah Bibi | Amnah Siddiqa | Jamil Ahmad | A. Holowatyj | Andreana N. Holowatyj | Iftikhar A. Sheikh | Rehan Zafar Paracha | Mukaram Khan | M. T. Saeed | Shahzina Kanwal | I. Sheikh | Rehan Zafar Paracha | Mukaram Khan | Jamil Ahmad
[1] Hidde de Jong,et al. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..
[2] Thomas Mestl,et al. FEEDBACK LOOPS, STABILITY AND MULTISTATIONARITY IN DYNAMICAL SYSTEMS , 1995 .
[3] F. Schreiber,et al. Centrality Analysis Methods for Biological Networks and Their Application to Gene Regulatory Networks , 2008, Gene regulation and systems biology.
[4] O Mason,et al. Graph theory and networks in Biology. , 2006, IET systems biology.
[5] Wengong Yu,et al. O-GlcNAcylation is a novel regulator of lung and colon cancer malignancy. , 2011, Biochimica et biophysica acta.
[6] D. Vocadlo,et al. Hyper-O-GlcNAcylation Is Anti-apoptotic and Maintains Constitutive NF-κB Activity in Pancreatic Cancer Cells* , 2013, The Journal of Biological Chemistry.
[7] Jun S. Song,et al. Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF. , 2013, Cancer cell.
[8] W. Yang,et al. Modification of p53 with O-linked N-acetylglucosamine regulates p53 activity and stability , 2006, Nature Cell Biology.
[9] O. Warburg. On respiratory impairment in cancer cells. , 1956, Science.
[10] D. Hanahan,et al. The Hallmarks of Cancer , 2000, Cell.
[11] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[12] Thomas A. Henzinger,et al. HYTECH: a model checker for hybrid systems , 1997, International Journal on Software Tools for Technology Transfer.
[13] J. Comet,et al. The SMBioNet Method for Discovering Models of Gene Regulatory Networks , 2009 .
[14] L. Cantley,et al. Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation , 2009, Science.
[15] M. Bryś,et al. Prediction of bladder cancer based on urinary content of MGEA5 and OGT mRNA level. , 2012, Clinical laboratory.
[16] Gerald W. Hart,et al. Cycling of O-linked β-N-acetylglucosamine on nucleocytoplasmic proteins , 2007, Nature.
[17] Galit Lahav,et al. Oscillations by the p53-Mdm2 feedback loop. , 2008, Advances in experimental medicine and biology.
[18] Peter A. Jones,et al. The Epigenomics of Cancer , 2007, Cell.
[19] John J Tyson,et al. Monitoring p53's pulse , 2004, Nature Genetics.
[20] Piero Fariselli,et al. Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure , 2011, BioData Mining.
[21] A. Gartel,et al. Transcriptional regulation of the p21((WAF1/CIP1)) gene. , 1999, Experimental cell research.
[22] M. V. Vander Heiden,et al. Aerobic glycolysis: meeting the metabolic requirements of cell proliferation. , 2011, Annual review of cell and developmental biology.
[23] Robert H. Costa,et al. Forkhead Box M1B Transcriptional Activity Requires Binding of Cdk-Cyclin Complexes for Phosphorylation-Dependent Recruitment of p300/CBP Coactivators , 2004, Molecular and Cellular Biology.
[24] Guy Karlebach,et al. Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.
[25] B. Gary,et al. Panepoxydone Targets NF-kB and FOXM1 to Inhibit Proliferation, Induce Apoptosis and Reverse Epithelial to Mesenchymal Transition in Breast Cancer , 2014, PloS one.
[26] Nobuyuki Tanaka,et al. p53 regulates glucose metabolism through an IKK-NF-κB pathway and inhibits cell transformation , 2008, Nature Cell Biology.
[27] Andrea Ciliberto,et al. Steady States and Oscillations in the p53/Mdm2 Network , 2005, Cell cycle.
[28] T. Lefebvre,et al. O-GlcNAcylation: A New Cancer Hallmark? , 2013, Front. Endocrinol..
[29] D. Hanahan,et al. Hallmarks of Cancer: The Next Generation , 2011, Cell.
[30] R. Costa,et al. Recruitment of p 300 / CBP Coactivators for Phosphorylation-Dependent Requires Binding of Cdk-Cyclin Complexes Forkhead Box M 1 B Transcriptional Activity , 2004 .
[31] W. Marston Linehan,et al. Reductive carboxylation supports growth in tumor cells with defective mitochondria , 2011, Nature.
[32] A. Levine,et al. Gain of function mutations in p53 , 1993, Nature Genetics.
[33] R. Milo,et al. Oscillations and variability in the p53 system , 2006, Molecular systems biology.
[34] G. Sethi,et al. Nutrient sensor O-GlcNAc transferase regulates breast cancer tumorigenesis through targeting of the oncogenic transcription factor FoxM1 , 2010, Oncogene.
[35] A. Mercurio,et al. ERβ regulation of NF-κB activation in prostate cancer is mediated by HIF-1 , 2015, Oncotarget.
[36] Xiaoyong Yang,et al. O-GlcNAc signaling in cancer metabolism and epigenetics. , 2015, Cancer letters.
[37] U. Sauer,et al. Coordination of microbial metabolism , 2014, Nature Reviews Microbiology.
[38] N. Tanaka,et al. Loss of p53 enhances catalytic activity of IKKβ through O-linked β-N-acetyl glucosamine modification , 2009, Proceedings of the National Academy of Sciences.
[39] Sung Soo Kim,et al. Cancer cell metabolism: implications for therapeutic targets , 2013, Experimental & Molecular Medicine.
[40] G. Hart,et al. Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc. , 1984, The Journal of biological chemistry.
[41] G. Hart,et al. O-GlcNAc signaling: a metabolic link between diabetes and cancer? , 2010, Trends in biochemical sciences.
[42] Michael Karin,et al. NF-kB as a Critical Link Between Inflammation and Cancer , 2009 .
[43] A. Thotakura,et al. Cancer: NF-κB regulates energy metabolism. , 2012, The international journal of biochemistry & cell biology.
[44] M. Pall. Gene-amplification model of carcinogenesis. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[45] M. Reginato,et al. mTOR/MYC Axis Regulates O-GlcNAc Transferase Expression and O-GlcNAcylation in Breast Cancer , 2015, Molecular Cancer Research.
[46] A. Puzio-Kuter,et al. The Role of p53 in Metabolic Regulation. , 2011, Genes & cancer.
[47] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[48] Adrien Richard,et al. Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. , 2004, Journal of theoretical biology.
[49] Karen H. Vousden,et al. Metabolic Regulation by p 53 Family Members , 2013 .
[50] Youn Wha Kim,et al. Regulatory role of p53 in cancer metabolism via SCO2 and TIGAR in human breast cancer. , 2012, Human pathology.
[51] M. Birnbaum,et al. The role of FoxO in the regulation of metabolism , 2008, Oncogene.
[52] Adrien Richard,et al. Formal Methods for Modeling Biological Regulatory Networks , 2006 .
[53] T. Halazonetis,et al. Genomic instability — an evolving hallmark of cancer , 2010, Nature Reviews Molecular Cell Biology.
[54] M. Roizen,et al. Hallmarks of Cancer: The Next Generation , 2012 .
[55] R. Ahmad,et al. Identification of the TP53-induced glycolysis and apoptosis regulator in various stages of colorectal cancer patients , 2015, Oncology reports.
[56] Feng Han,et al. Tumor and Stem Cell Biology Cancer Research GlcNAcylation Plays an Essential Role in Breast Cancer Metastasis , 2010 .
[57] Qianqian Zhu,et al. O-GlcNAcylation plays a role in tumor recurrence of hepatocellular carcinoma following liver transplantation , 2012, Medical Oncology.
[58] Uri Alon,et al. Dynamics of the p53-Mdm2 feedback loop in individual cells , 2004, Nature Genetics.
[59] H. Dvorak. Tumors: wounds that do not heal. Similarities between tumor stroma generation and wound healing. , 1986, The New England journal of medicine.
[60] Marco Pistore,et al. NuSMV 2: An OpenSource Tool for Symbolic Model Checking , 2002, CAV.
[61] M. Kaufman,et al. From structure to dynamics: frequency tuning in the p53-Mdm2 network I. Logical approach. , 2009, Journal of theoretical biology.
[62] R. Deberardinis,et al. Beyond aerobic glycolysis: Transformed cells can engage in glutamine metabolism that exceeds the requirement for protein and nucleotide synthesis , 2007, Proceedings of the National Academy of Sciences.
[63] G. Parker,et al. Regulation of Akt signaling by O-GlcNAc in euglycemia. , 2008, American journal of physiology. Endocrinology and metabolism.
[64] D. Burk,et al. On respiratory impairment in cancer cells. , 1956, Science.
[65] R. Thomas,et al. Boolean formalization of genetic control circuits. , 1973, Journal of theoretical biology.
[66] Guido Kroemer,et al. Tumor cell metabolism: cancer's Achilles' heel. , 2008, Cancer cell.
[67] T. Mak,et al. Regulation of cancer cell metabolism , 2011, Nature Reviews Cancer.
[68] Benno Schwikowski,et al. Graph-based methods for analysing networks in cell biology , 2006, Briefings Bioinform..
[69] W. Dias,et al. O-GlcNAcylation: The Sweet Side of the Cancer , 2014, Front. Oncol..
[70] R. Thomas,et al. Logical analysis of systems comprising feedback loops. , 1978, Journal of theoretical biology.
[71] M. Bryś,et al. Expression of genes encoding for enzymes associated with O-GlcNAcylation in endometrial carcinomas: clinicopathologic correlations. , 2012, Ginekologia polska.
[72] R. Moreno-Sánchez,et al. Dual regulation of energy metabolism by p53 in human cervix and breast cancer cells. , 2015, Biochimica et biophysica acta.
[73] U Alon,et al. Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[74] T. Soussi,et al. TP53: an oncogene in disguise , 2015, Cell Death and Differentiation.
[75] Chi V Dang,et al. MYC on the Path to Cancer , 2012, Cell.
[76] Didier Lime,et al. Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks with Delays , 2007, Complexus.
[77] David T. W. Jones,et al. Signatures of mutational processes in human cancer , 2013, Nature.
[78] M. Bryś,et al. Gene expression of O-GlcNAc cycling enzymes in human breast cancers , 2011, Clinical and Experimental Medicine.
[79] Franck Delaplace,et al. Semantics of Biological Regulatory Networks , 2007, Electron. Notes Theor. Comput. Sci..
[80] Michael Naumann,et al. Dynamics of p53 and NF-κB regulation in response to DNA damage and identification of target proteins suitable for therapeutic intervention , 2012, BMC Systems Biology.
[81] F. A. La Rosa,et al. Differential regulation of the c-myc oncogene promoter by the NF-kappa B rel family of transcription factors , 1994, Molecular and cellular biology.
[82] Thomas A. Henzinger,et al. HYTECH: A Model Checker for Hybrid Systems , 1997, CAV.
[83] M. Reginato,et al. Critical Role of O-Linked β-N-Acetylglucosamine Transferase in Prostate Cancer Invasion, Angiogenesis, and Metastasis* , 2012, The Journal of Biological Chemistry.
[84] K. Vosseller,et al. O-GlcNAc in cancer biology , 2013, Amino Acids.
[85] Jamil Ahmad,et al. A parallel approach for accelerated parameter identification of Gene Regulatory Networks , 2014, IWBBIO.
[86] G. Semenza,et al. Hypoxia-Inducible Factor 1 (HIF-1) Pathway , 2007, Science's STKE.
[87] Jing Zhao,et al. Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis , 2012, BMC Systems Biology.
[88] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[89] P. Pelicci,et al. Oxidative stress activates a specific p53 transcriptional response that regulates cellular senescence and aging , 2013, Aging cell.
[90] Jamil Ahmad,et al. On the modelling and analysis of the regulatory network of dengue virus pathogenesis and clearance , 2014, Comput. Biol. Chem..
[91] M. Disis. Immune regulation of cancer. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[92] U. Niazi,et al. Formal Modeling and Analysis of the MAL-Associated Biological Regulatory Network: Insight into Cerebral Malaria , 2012, PloS one.
[93] Karen H. Vousden,et al. Metabolic regulation by p53 , 2011, Journal of Molecular Medicine.
[94] D. Sabatini,et al. Cancer Cell Metabolism: Warburg and Beyond , 2008, Cell.
[95] N. Perkins. Achieving transcriptional specificity with nf-κb , 1997 .
[96] René Thomas. Regulatory networks seen as asynchronous automata: A logical description , 1991 .
[97] Ralph J Deberardinis,et al. Brick by brick: metabolism and tumor cell growth. , 2008, Current opinion in genetics & development.
[98] Alberto Mantovani,et al. Cancer-related inflammation, the seventh hallmark of cancer: links to genetic instability. , 2009, Carcinogenesis.
[99] O. Warburg. On the origin of cancer cells. , 1956, Science.
[100] D. E. Atkinson,et al. Biological feedback control at the molecular level. , 1965, Science.
[101] Stanley Wasserman,et al. Social Network Analysis: Methods and Applications , 1994, Structural analysis in the social sciences.
[102] Chris Albanese,et al. NF-κB Controls Cell Growth and Differentiation through Transcriptional Regulation of Cyclin D1 , 1999, Molecular and Cellular Biology.
[103] Flore Kruiswijk,et al. p53 in survival, death and metabolic health: a lifeguard with a licence to kill , 2015, Nature Reviews Molecular Cell Biology.
[104] O. Warburg,et al. Über die Oxydationen in lebenden Zellen nach Versuchen am Seeigelei , 1910 .
[105] V. Potter. The biochemical approach to the cancer problem. , 1958, Federation proceedings.
[106] A. Levine,et al. Proliferation and tissue remodeling in cancer: the hallmarks revisited , 2012, Cell Death and Disease.
[107] Gerald C. Chu,et al. Oncogenic Kras Maintains Pancreatic Tumors through Regulation of Anabolic Glucose Metabolism , 2012, Cell.
[108] I. Mills,et al. O-GlcNAc transferase integrates metabolic pathways to regulate the stability of c-MYC in human prostate cancer cells. , 2013, Cancer research.
[109] R. Thomas,et al. Dynamical behaviour of biological regulatory networks--II. Immunity control in bacteriophage lambda. , 1995, Bulletin of mathematical biology.
[110] Carlos Cordon-Cardo,et al. At the Crossroads of Inflammation and Tumorigenesis , 1999, The Journal of experimental medicine.
[111] Jamil Ahmad. Modélisation hybride et analyse des dynamiques des réseaux de régulations biologiques en tenant compte des délais , 2009 .
[112] Aurélien Naldi,et al. Logical modelling of gene regulatory networks with GINsim. , 2012, Methods in molecular biology.
[113] T. Issad,et al. O-GlcNAc modification of transcription factors, glucose sensing and glucotoxicity , 2008, Trends in Endocrinology & Metabolism.
[114] Chi V. Dang,et al. The interplay between MYC and HIF in cancer , 2008, Nature Reviews Cancer.
[115] J. Schmid,et al. The complexity of NF-κB signaling in inflammation and cancer , 2013, Molecular Cancer.
[116] Reinhard Schneider,et al. Using graph theory to analyze biological networks , 2011, BioData Mining.
[117] P. Ernst,et al. Review article: the role of inflammation in the pathogenesis of gastric cancer , 1999, Alimentary pharmacology & therapeutics.
[118] René Thomas,et al. Logical identification of all steady states: The concept of feedback loop characteristic states , 1993 .
[119] R. Gillies,et al. Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function. , 2015, Cancer research.
[120] Tom Walsh,et al. Ten genes for inherited breast cancer. , 2007, Cancer cell.