Screening for genes and subnetworks associated with atypical teratoid/rhabdoid tumors using bioinformatics analysis

References

• Liao P, Finlay JL, Stearns DS, et al. Alex’s Lemonade Stand Foundation infant and childhood primary brain and central nervous system tumors diagnosed in the United States in 2007–2011. Neuro Oncol. 2015;16(Suppl 10):x1–x36.
   PubMedGoogle Scholar
• Frühwald MC, Biegel JA, Bourdeaut F, et al. Atypical teratoid/rhabdoid tumors-current concepts, advances in biology, and potential future therapies. Neuro Oncol. 2016;18(6):764–778.
   PubMed Web of Science ®Google Scholar
• Burger PC, Yu I-T, Tihan T, et al. Atypical teratoid/rhabdoid tumor of the central nervous system: a highly malignant tumor of infancy and childhood frequently mistaken for medulloblastoma: a Pediatric Oncology Group study. Am J Surg Pathol. 1998;22(9):1083–1092.
   PubMed Web of Science ®Google Scholar
• Ho DM, Hsu C, Wong T, et al. Atypical teratoid/rhabdoid tumor of the central nervous system: a comparative study with primitive neuroectodermal tumor/medulloblastoma. Acta Neuropathol. 2000;99(5):482–488.
   PubMed Web of Science ®Google Scholar
• Packer RJ, Biegel JA, Blaney S, et al. Atypical teratoid/rhabdoid tumor of the central nervous system: report on workshop. J Pediatr Hematol Oncol. 2002;24(5):337–342.
   PubMed Web of Science ®Google Scholar
• Hilden JM, Meerbaum S, Burger P, et al. Central nervous system atypical teratoid/rhabdoid tumor: results of therapy in children enrolled in a registry. J Clin Oncol. 2004;22(14):2877–2884.
   PubMed Web of Science ®Google Scholar
• Lafay-Cousin L, Hawkins C, Carret AS, et al. Central nervous system atypical teratoid rhabdoid tumours: the Canadian Paediatric Brain Tumour Consortium experience. Eur J Cancer. 2012;48(3):353–359.
   PubMed Web of Science ®Google Scholar
• Louis DN, Perry A, Reifenberger G, et al. The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary. Acta Neuropathol. 2016;131(6):803–820.
   PubMed Web of Science ®Google Scholar
• Fischer-Valuck BW, Chen I, Srivastava AJ, et al. Assessment of the treatment approach and survival outcomes in a modern cohort of patients with atypical teratoid rhabdoid tumors using the National Cancer Database. Cancer. 2017;123(4):682–687.
   PubMed Web of Science ®Google Scholar
• Biswas A, Kashyap L, Kakkar A, et al. Atypical teratoid/rhabdoid tumors: challenges and search for solutions. Cancer Manag Res. 2016;8:115–125.
   PubMed Web of Science ®Google Scholar
• Chi SN, Zimmerman MA, Yao X, et al. Intensive multimodality treatment for children with newly diagnosed CNS atypical teratoid rhabdoid tumor. J Clin Oncol. 2009;27(3):385–389.
   PubMed Web of Science ®Google Scholar
• Kumar R, Liu APY, Orr BA, et al. Advances in the classification of pediatric brain tumors through DNA methylation profiling: from research tool to frontline diagnostic. Cancer. 2018;124(21):4168–4180.
   PubMed Web of Science ®Google Scholar
• Gajjar A, Stefan MP, Taylor MD, et al. Molecular insights into pediatric brain tumors have the potential to transform therapy. Clin Cancer Res. 2014;20(22):5630–5641.
   PubMed Web of Science ®Google Scholar
• Morris JA, Gayther SA, Jacobs IJ, et al. A suite of Perl modules for handling microarray data. Bioinformatics. 2008;24(8):1102–1103.
   PubMed Web of Science ®Google Scholar
• Lin SM, Du P, Huber W, et al. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 2008;36:1–9.
   PubMed Web of Science ®Google Scholar
• Carvalho BS, Irizarry RA. A framework for oligonucleotide microarray preprocessing. Bioinformatics. 2010;26(19):2363–2367.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
   PubMed Web of Science ®Google Scholar
• Ogata H, Goto S, Sato K, et al. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999;27(1):29–34.
   PubMed Web of Science ®Google Scholar
• Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006;34:D322–D326.
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, et al. cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11–S17.
   PubMed Web of Science ®Google Scholar
• Geng R, Li N, Xu Y, et al. Identification of core biomarkers associated with outcome in glioma: evidence from bioinformatics analysis. Dis Markers. 2018;2018:3215958.
   PubMed Web of Science ®Google Scholar
• Yang G, Chen Q, Xiao J, et al. Identification of genes and analysis of prognostic values in nonsmoking females with non-small cell lung carcinoma by bioinformatics analyses. Cancer Manag Res. 2018;10:4287–4295.
   PubMed Web of Science ®Google Scholar
• Ni M, Liu X, Wu J, et al. Identification of candidate biomarkers correlated with the pathogenesis and prognosis of non-small cell lung cancer via integrated bioinformatics analysis. Front Genet. 2018;9:469.
   PubMed Web of Science ®Google Scholar
• Sang L, Wang X-M, Xu D-Y, et al. Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma. World J Gastroenterol. 2018;24(24):2605–2616.
   PubMed Web of Science ®Google Scholar
• Evan GI, Vousden KH. Proliferation, cell cycle and apoptosis in cancer. Nature. 2001;411(6835):342–348.
   PubMed Web of Science ®Google Scholar
• Xie B, Wang S, Jiang N, et al. Cyclin B1/CDK1-regulated mitochondrial bioenergetics in cell cycle progression and tumor resistance. Cancer Lett. 2019;443:56–66.
   PubMed Web of Science ®Google Scholar
• Dong S, Huang F, Zhang H, et al. Overexpression of BUB1B, CCNA2, CDC20, and CDK1 in tumor tissues predicts poor survival in pancreatic ductal adenocarcinoma. Biosci Rep. 2019;39:BSR20182306.
   PubMed Web of Science ®Google Scholar
• Sung WW, Lin YM, Wu PR, et al. High nuclear/cytoplasmic ratio of Cdk1 expression predicts poor prognosis in colorectal cancer patients. BMC Cancer. 2014;14:951.
   PubMed Web of Science ®Google Scholar
• Ito Y, Takeda T, Sakon M, et al. Expression and prognostic role of cyclin-dependent kinase 1 (cdc2) in hepatocellular carcinoma. Oncology. 2000;59(1):68–74.
   PubMed Web of Science ®Google Scholar
• Hongo F, Takaha N, Oishi M, et al. CDK1 and CDK2 activity is a strong predictor of renal cell carcinoma recurrence. Urol Oncol. 2014;32(8):1240–1246.
   PubMed Web of Science ®Google Scholar
• Kim DH, Park SE, Kim M, et al. A functional single nucleotide polymorphism at the promoter region of cyclin A2 is associated with increased risk of colon, liver, and lung cancers. Cancer. 2011;117(17):4080–4091.
   PubMed Web of Science ®Google Scholar
• Gan Y, Li Y, Li T, et al. CCNA2 acts as a novel biomarker in regulating the growth and apoptosis of colorectal cancer. Cancer Manag Res. 2018;10:5113–5124.
   PubMed Web of Science ®Google Scholar
• Weinstein J, Jacobsen FW, Hsu-Chen J, et al. A novel mammalian protein, p55CDC, present in dividing cells is associated with protein kinase activity and has homology to the Saccharomyces cerevisiae cell division cycle proteins Cdc20 and Cdc4. Mol Cell Biol. 1994;14(5):3350–3363.
   PubMed Web of Science ®Google Scholar
• Ding Y, Yu S, Bao Z, et al. CDC20 with malignant progression and poor prognosis of astrocytoma revealed by analysis on gene expression. J Neurooncol. 2017;133(1):87–95.
   PubMed Web of Science ®Google Scholar
• Choi JW, Kim Y, Lee JH, et al. High expression of spindle assembly checkpoint proteins CDC20 and MAD2 is associated with poor prognosis in urothelial bladder cancer. Virchows Arch. 2013;463(5):681–687.
   PubMed Web of Science ®Google Scholar
• Wang L, Zhang J, Wan L, et al. Targeting Cdc20 as a novel cancer therapeutic strategy. Pharmacol Ther. 2015;151:141–151.
   PubMed Web of Science ®Google Scholar
• Watt PM, Hickson ID. Structure and function of type II DNA topoisomerases. Biochem J. 1994;303(3):681–695.
   PubMed Web of Science ®Google Scholar
• Zhang R, Xu J, Zhao J, et al. Proliferation and invasion of colon cancer cells are suppressed by knockdown of TOP2A. J Cell Biochem. 2018;119(9):7256–7263.
   PubMed Web of Science ®Google Scholar
• Pei Y, Yin X, Liu X. TOP2A induces malignant character of pancreatic cancer through activating β-catenin signaling pathway. Biochim Biophys Acta Mol Basis Dis. 2018;1864(1):197–207.
   PubMed Web of Science ®Google Scholar
• Supernat A, Lapińska-Szumczyk S, Majewska H, et al. Tumor heterogeneity at protein level as an independent prognostic factor in endometrial cancer. Transl Oncol. 2014;7(5):613–619.
   PubMed Web of Science ®Google Scholar
• Otto T, Sicinski P. Cell cycle proteins as promising targets in cancer therapy. Nat Rev Cancer. 2017;17(2):93–115.
   PubMed Web of Science ®Google Scholar