Protein–protein interaction networks and different clustering analysis in Burkitt’s lymphoma

References

• Yustein JT, Dang CV. Biology and treatment of Burkitt's lymphoma. Curr Opin Hematol. 2007;14(4):375–381. PMID:17534164. doi: 10.1097/MOH.0b013e3281bccdee
   PubMed Web of Science ®Google Scholar
• Trzeciecka A, Klossowski S, Bajor M, et al. Dimeric peroxiredoxins are druggable targets in human Burkitt lymphoma. Oncotarget. 2016;7(2):1717–1731. PMID:26636537. doi: 10.18632/oncotarget.6435
   PubMed Web of Science ®Google Scholar
• Campanero MR. Mechanisms involved in Burkitt’s lymphoma tumor formation. Clin Transl Oncol. 2008;10(5):250–255. PMID:18490240. doi: 10.1007/s12094-008-0193-x
   PubMed Web of Science ®Google Scholar
• Xenarios I, Salwínski L, Duan XJ, et al. DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002;30(1):303–305. PMID:11752321. doi: 10.1093/nar/30.1.303
   PubMed Web of Science ®Google Scholar
• Yu L, Gao L, Sun PG. Research on algorithms for complexes and functional modules prediction in protein-protein interaction networks. Chin J Comput. 2011;34(7):1239–1251. doi: 10.3724/SP.J.1016.2011.01239
   Google Scholar
• Liu H, Liao B, Peng LH. Research of clustering algorithms in protein-protein interaction network. Comput Eng Applic. 2008;44(30):142–144.
   Google Scholar
• Ramadan E, Naef A, Ahmed M. Protein complexes predictions within protein interaction networks using genetic algorithms. BMC Bioinformatics. 2016;17(Suppl 7):269, PMID:27454228. doi: 10.1186/s12859-016-1096-4
   PubMedGoogle Scholar
• Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Database issue):D561–D568. PMID:21045058. doi: 10.1093/nar/gkq973
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. PMID:14597658. doi: 10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Huang DA, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57. PMID:19131956. doi: 10.1038/nprot.2008.211
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Tan Q, et al. The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007;8(9):R183, PMID:17784955. doi: 10.1186/gb-2007-8-9-r183
   PubMed Web of Science ®Google Scholar
• Burkard TR, Rix U, Breitwieser FP, et al. A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PLoS Comput Biol. 2010;6(11):e1001001, PMID:21124949. doi: 10.1371/journal.pcbi.1001001
   PubMed Web of Science ®Google Scholar
• Stelzl U, Worm U, Lalowski M. A human protein-protein interaction network: a resource for annotating the proteome. Cell. 2005;122(6):957–968. PMID:16169070. doi: 10.1016/j.cell.2005.08.029
   PubMed Web of Science ®Google Scholar
• Bosque G, Folch-Fortuny A, Picó J, et al. Topology analysis and visualization of potyvirus protein-protein interaction network. BMC Syst Biol. 2014;8:205. PMID: 25409737. doi: 10.1186/s12918-014-0129-8
   Web of Science ®Google Scholar
• Yellapu NK, Pulaganti M, Pakala SB. Bioinformatics exploration of PAK1 (P21-activated kinase-1) revealed potential network gene elements in breast invasive carcinoma. J Biomol Struct Dyn. 2017;35(10):2269–2279. PMID:27456030. doi: 10.1080/07391102.2016.1216894
   PubMed Web of Science ®Google Scholar
• Ma T, Tan C, Zhang H, et al. Bridging the gap between traditional Chinese medicine and systems biology: the connection of cold syndrome and NEI network. Mol Biosyst. 2010;6(4):613–619. PMID:20237638. doi: 10.1039/b914024g
   PubMed Web of Science ®Google Scholar
• Keane H, Ryan BJ, Jackson B, et al. Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson’s disease. Sci Rep. 2015;5:17004, PMID:26608097. doi: 10.1038/srep17004
   PubMed Web of Science ®Google Scholar
• Gu J, Chen Y, Li S, et al. Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Syst Biol. 2010;4:47. PMID:20406493. doi: 10.1186/1752-0509-4-47
   PubMed Web of Science ®Google Scholar
• Pan J, Cong Z, Zhong M, et al. Analysis of hepatocellular carcinoma and metastatic hepatic carcinoma via functional modules in a protein–protein interaction network. J Cancer Res Ther. 2014;10 Suppl(7):C186–C194.
   PubMed Web of Science ®Google Scholar
• Wang J, Zhong J, Chen G, et al. Clusterviz: a cytoscape APP for cluster analysis of biological network. IEEE/ACM Trans Comput Biol Bioinform. 2015;12(4):815–822. PMID:26357321. doi: 10.1109/TCBB.2014.2361348
   PubMed Web of Science ®Google Scholar
• Wang ZH, Dong YY, Wang XY. Review on several clustering methods in protein-protein interaction network. J Nat Univ Def Technol. 2009;31(4):81–86.
   Google Scholar
• Ji JZ, Liu ZJ, Liu HX, et al. An overview of research on functional module detection for protein-protein interaction networks. Acta Autom Sin. 2014;40(4):577–593.
   Google Scholar
• Li J, Zhao PX. Mining functional modules in heterogeneous biological networks using multiplex pagerank approach. Front Plant Sci. 2016;7:903. PMID:27446133.
   PubMed Web of Science ®Google Scholar
• Altafuiamin M, Shinbo Y, Mihara K, et al. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics. 2006;7:207. PMID:16613608. doi: 10.1186/1471-2105-7-207
   PubMed Web of Science ®Google Scholar
• Tang Y, Li M. A cytoscape plugin for visualization and clustering analysis of protein interaction networks. Chin J Bioinform. 2014;12(1):38–45.
   Google Scholar
• Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003;4:2. PMID:12525261. doi: 10.1186/1471-2105-4-2
   PubMed Web of Science ®Google Scholar
• Wang J, Li M, Deng Y, et al. Recent advances in clustering methods for protein interaction networks. BMC Genomics. 2010;11(Suppl 3):S10. PMID:21143777. doi: 10.1186/1471-2164-11-S3-S10
   PubMedGoogle Scholar
• Shen HW, Cheng XQ, Cai K, et al. Detect overlapping and hierarchical community structure in networks. Physica A. 2009;388(8):1706–1712. doi: 10.1016/j.physa.2008.12.021
   Web of Science ®Google Scholar
• Cai J, Wang JX, Li M, et al. Clusterviz: a cytoscape plugin for clustering visualization. China J Bioinform. 2011;9(3):185–188.
   Google Scholar
• Yang LM, Ott G, Jaffe E, et al. Molecular diagnosis of Burkitt’s lymphoma. N Engl J Med. 2006;354(23):2431–2442. PMID:16760443. doi: 10.1056/NEJMoa055759
   PubMed Web of Science ®Google Scholar
• Müller JR, Janz S, Goedert JJ, et al. Persistence of immunoglobulin heavy chain/c-myc recombination-positive lymphocyte clones in the blood of human immunodeficiency virus-infected homosexual men. Proc Natl Acad Sci U S A. 1995;92(14):6577–6581. PMID:7604036. doi: 10.1073/pnas.92.14.6577
   PubMed Web of Science ®Google Scholar
• Pelengaris S, Khan M, Evan G. c-MYC: more than just a matter of life and death. Nat Rev Cancer. 2002;2(10):764–776. PMID:12360279. doi: 10.1038/nrc904
   PubMed Web of Science ®Google Scholar
• Rowe M, Fitzsimmons L, Bell AI. Epstein–Barr virus and Burkitt lymphoma. Chin J Cancer. 2014;33(12):609–619. PMID:25418195.
   PubMed Web of Science ®Google Scholar
• Hasegawa H, Yamada Y, Iha H, et al. Activation of p53 by Nutlin-3a, an antagonist of MDM2, induces apoptosis and cellular senescence in adult T-cell leukemia cells. Leukemia. 2009;23(11):2090–2101. PMID:19710698. doi: 10.1038/leu.2009.171
   PubMed Web of Science ®Google Scholar
• Feng Z, Levine A. The regulation of energy metabolism and the IGF-1/mTOR pathways by the p53 protein. Trends Cell Biol. 2010;20(7):427–434. PMID:20399660. doi: 10.1016/j.tcb.2010.03.004
   PubMed Web of Science ®Google Scholar
• Li Z, Gonzalez CL, Wang B, et al. Cdkn2a suppresses metastasis in squamous cell carcinomas induced by the gain-of-function mutant p53 R172H. J Pathol. 2016;240(2):224–234. PMID:27447534. doi: 10.1002/path.4770
   PubMed Web of Science ®Google Scholar
• Pervez S, Nasir MI, Moatter T, et al. Characterization of genetic lesions inapoptosis-regulating and proliferation control genes in diffuse large B-cell non-Hodgkin’s lymphoma. J Cancer Res Ther. 2009;5(4):254–262. PMID: 20160358. doi: 10.4103/0973-1482.59901
   PubMed Web of Science ®Google Scholar
• Tu DP, Ma XJ, Mo CM, et al. Progress and bioinformatics analysis of FOS protein. Hubei Agr Sci. 2015;54(7):1537–1542.
   Google Scholar
• Conticello C, Pedini F, Zeuner A, et al. IL-4 protects tumor cells from anti-CD95 and chemotherapeutic agents via up-regulation of antiapoptotic proteins. J Immunol. 2004;172(9):5467–5477. PMID:15100288. doi: 10.4049/jimmunol.172.9.5467
   PubMed Web of Science ®Google Scholar
• Palma MD. Partners in crime: VEGF and IL-4 conscript tumour-promoting macrophages. J Pathol. 2012;227(1):4–7. PMID:22367978. doi: 10.1002/path.4008
   PubMed Web of Science ®Google Scholar
• Sun B, Han DS. Negative regulation of toll-like receptors signaling pathways. Prog Biochem Biophys. 2009;36(12):1516–1522. doi: 10.3724/SP.J.1206.2009.00213
   Web of Science ®Google Scholar
• Chen LL, Shi WY, You XF. Study on the role and its mechanism of Ibrutinib in inhibiting proliferation and inducing apoptosis in Burkitt’s lymphoma cell line. Med J Commun. 2016;30(1):24–28.
   Google Scholar