Using evolutional properties of gene networks in understanding survival prognosis of glioblastoma

IEEE Journal of Biomedical and Health Informatics

Volumn 18, Issue 3, 2014, Pages 810-816

  Upton, Alex ^a   Arvanitis, Theodoros N ^a,b  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Cancer evolution; Gene regulatory network; genomics; glioblastoma; glioblastoma evolution; graph theory

Indexed keywords

CELL CULTURE; DISEASES; GENES;

ABSOLUTE CORRELATIONS; CANCER EVOLUTION; EVOLUTIONAL PROPERTIES; GENE REGULATORY NETWORKS; GENOMICS; GLIOBLASTOMAS; REGULATORY INTERACTIONS; TOPOLOGICAL PROPERTIES;

GRAPH THEORY;

ALGORITHM; BRAIN NEOPLASMS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; GENOMICS; GLIOBLASTOMA; HUMAN; METABOLISM; PROCEDURES; PROGNOSIS; SURVIVAL; TUMOR CELL LINE;

ALGORITHMS; BRAIN NEOPLASMS; CELL LINE, TUMOR; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENOMICS; GLIOBLASTOMA; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; SURVIVAL ANALYSIS;

EID: 84900838089     PISSN: 21682194     EISSN: None     Source Type: Journal    
DOI: 10.1109/JBHI.2013.2282569     Document Type: Article

References (28)

1. A. Margolin, I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Favera, and A. Califano, "ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context, " BMC Bioinformat., vol. 7, p. S7, 2006.
2. J. Schaefer and K. Strimmer, "An empirical Bayes approach to inferring large-scale gene association networks, " Bioinformatics, vol. 21, pp. 754-764, 2005.
3. P. Langfelder and S. Horvath, "WGCNA: An R package for weighted correlation network analysis, " BMC Bioinformat., vol. 9, p. 559, 2008.
4. A. Upton and T. N. Arvanitis, "Investigating survival prognosis of glioblastoma using evolutional properties of gene networks, " in Proc. IEEE 12th Int. Conf. Bioinformat. Bioeng., 2012, pp. 466-471.
5. S.Horvath, B.Zhang, M.Carlson, K.Lu, S.Zhu, R.Felciano, M.Laurance, W. Zhao, Q. Shu, Y. Lee, A. Scheck, L. Liau, H. Wu, D. Geschwind, P. Febbo, H.Kornblum, T.Cloughesy, S. Nelson, andP.Mischel, "Analysis of oncogenic signaling networks in Glioblastoma identifies ASPM as a novel molecular target, " Proc. Natl. Acad. Sci. USA, vol. 103, pp. 17402-17407, 2006.
6. E. G. Van Meir, C. G. Hadjipanayis, A. D. Norden, H.-K. Shu, P. Y. Wen, and J. J. Olson, "Exciting new advances in neuro-oncology: The avenue to a cure for malignant glioma, " CA Cancer J. Clin., vol. 60, pp. 166-193, 2010.
7. R. G. W. Verhaak, K. A. Hoadley, E. Purdom, V. Wang, Y. Qi, M. D. Wilkerson, C. R. Miller, L. Ding, T. Golub, J. P. Mesirov, G. Alexe, M. Lawrence, M. O'Kelly, P. Tamayo, B. A. Weir, S. Gabriel, W. Winckler, S. Gupta, L. Jakkula, H. S. Feiler, J. G. Hodgson, C. D. James, J. N. Sarkaria, C. Brennan, A. Kahn, P. T. Spellman, R. K. Wilson, T. P. Speed, J. W. Gray, M. Meyerson, G. Getz, C. M. Perou, and D. N. Hayes, "Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1, " Cancer cell, vol. 17, pp. 98-110, 2010.
8. R. A. Irizarry, B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs, and T. P. Speed, "Summaries of affymetrix genechip probe level data, " Nucleic Acids Res., vol. 31, p. e15, Feb. 15, 2003.
9. R. Ihaka and R. Gentleman, "R: A language for data analysis and graphics, " J. Comput. Graphical Statist., vol. 5, pp. 299-314, 1996.
10. M. E. J. Newman, "The structure and function of complex networks, " SIAM Rev., vol. 45, pp. 167-256, 2003.
11. S. Bergmann, J. Ihmels, and N. Barkai, "Similarities and differences in genome-wide expression data of six organisms, " PLoS Biol, vol. 2, p. e9, 2003.
12. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi, "Hierarchical organization of modularity in metabolic networks, " Science, vol. 297, pp. 1551-5, 2002.
13. B. Zhang and S. Horvath, "A general framework for weighted gene co-expression network analysis, " Stat. Appl. Genet. Mol. Biol., vol. 4, 2005, Article 17.
14. G. Csardi and T. Nepusz, "The igraph software package for complex network research, " InterJournal Complex Syst., vol. 1695, 2006.
15. L. Freeman, "Centrality in social networks: Conceptual clarification, " Social Netw., vol. 1, pp. 215-239, 1978.
16. L. Freeman, "A set of measures of centrality based on betweenness, " Sociometry, vol. 40, pp. 35-41, 1977.
17. R. McLendon, A. Friedman, D. Bigner, E. G. Van Meir, D. J. Brat, G. M. Mastrogianakis, J. J. Olson, T. Mikkelsen, N. Lehman, and K. Aldape, "Comprehensive genomic characterization defines human glioblastoma genes and core pathways, " Nature, vol. 455, pp. 1061-1068, 2008.
18. G. Gundem, C. Perez-Llamas, A. Jene-Sanz, A. Kedzierska, A. Islam, J. Deu-Pons, S. Furney, and N. Lopez-Bigas, "IntOGen: Integration and data-mining of multidimensional oncogenomic data, " Nature Methods, vol. 7, pp. 92-93, 2010.
19. S. J. Furney, B. Calvo, P. Larranaga, J. A. Lozano, and N. Lopez-Bigas, "Prioritization of candidate cancer genes-An aid to oncogenomic studies, " Nucleic Acids Res., vol. 36, p. e115, Oct. 1, 2008.
20. P. Fiorenzo, M. P. Mongiardi, D. Dimitri, M. Cozzolino, A. Ferri, N. Montano, G. Trevisi, G. Maira, L. Battistini, M. L. Falchetti, A. Levi, and R. Pallini, "HIF1-positive and HIF1-negative glioblastoma cells compete in vitro but cooperate in tumor growth in vivo, " Int. J. oncol., vol. 36, pp. 785-791, 2010.
21. S. A. Forbes, N. Bindal, S. Bamford, C. Cole, C. Y. Kok, D. Beare, M. Jia, R. Shepherd, K. Leung, A. Menzies, J. W. Teague, P. J. Campbell, M. R. Stratton, and P. A. Futreal, "COSMIC: Mining complete cancer genomes in the catalogue of somatic mutations in cancer, " Nucleic Acids Res., vol. 39, pp. D945-D950, Jan. 1, 2011.
22. M. Kanamori, T. Kawaguchi, J. M. Nigro, B. G. Feuerstein, M. S. Berger, L. Miele, and R. O. Pieper, "Contribution of notch signaling activation to human glioblastoma multiforme, " J. Neurosurg., vol. 106, pp. 417-427, 2007.
23. C. Brennan, H. Momota, D. Hambardzumyan, T. Ozawa, A. Tandon, A. Pedraza, and E. Holland, "Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations, " PLoS ONE, vol. 4, p. e7752, 2009.
24. N. G. Thaker, F. Zhang, P. R. McDonald, T. Y. Shun, M. D. Lewen, I. F. Pollack, and J. S. Lazo, "Identification of survival genes in human glioblastoma cells by small interfering RNA screening, " Molecular Pharmacol., vol. 76, pp. 1246-1255, Dec. 1, 2009.
25. A. B. Hjelmeland, Q. Wu, S. Wickman, C. Eyler, J. Heddleston, Q. Shi, J. D. Lathia, J. MacSwords, J. Lee, R. E. McLendon, and J. N. Rich, "Targeting A20 decreases glioma stem cell survival and tumor growth, " PLoS Biol., vol. 8, p. e1000319, 2010.
26. H. Huang, Y. Xiang, B. Su, W. Xiong, and X. Zhang, "Potential roles for Gfi1 in the pathogenesis and proliferation of glioma, " Med. Hypotheses, vol. 80, pp. 629-632, 2013.
27. O. Mendez, J. Zavadil, M. Esencay, Y. Lukyanov, D. Santovasi, S.-C. Wang, E. Newcomb, and D. Zagzag, "Knock down of HIF-1alpha in glioma cells reduces migration in vitro and invasion in vivo and impairs their ability to form tumor spheres, " Molecular Cancer, vol. 9, p. 133, 2010.
28. A. Mangiola, N. Saulnier, P. De Bonis, D. Orteschi, G. Sica, G. Lama, B. L. Pettorini, G. Sabatino, M. Zollino, L. Lauriola, A. Colabianchi, G. Proietti, G. Kovacs, G. Maira, and C. Anile, "Gene expression profile of glioblastoma peritumoral tissue: An ex vivo study, " PLoS ONE, vol. 8, p. e57145, 2013.