Identifying mutated core modules in glioblastoma by integrative network analysis

2012 IEEE 6th International Conference on Systems Biology, ISB 2012

Volumn , Issue , 2012, Pages 304-309

  Zhang, Junhua ^a   Zhang, Shihua ^a   Wang, Yong ^a   Zhao, Junfei ^a   Zhang, Xiang Sun ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Cancer; core module; gene expression; somatic mutation

Indexed keywords

BRAIN TUMORS; CANCER; CANCER BIOLOGY; CANCER GENOME; CANDIDATE GENES; CORE MODULE; FUNCTIONAL MODULES; GLIOBLASTOMA MULTIFORME; GLIOBLASTOMAS; NETWORK-BASED; OPTIMIZATION MODELS; PRIOR INFORMATION; SOMATIC MUTATION; SUBNETWORKS; TUMOR PATIENT; TUMOR SUPPRESSORS;

BIOLOGY; DISEASES; GENE EXPRESSION; ONCOGENIC VIRUSES;

TUMORS;

EID: 84868640750     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISB.2012.6314154     Document Type: Conference Paper

References (43)

1. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
2. International cancer genome consortium. International network of cancer genome projects. Nature 464, 993-998 (2010).
3. M. Meyerson, S. Gabriel and G. Getz, Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11, 685-696 (2010).
4. C. Greenman et al., Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158 (2007).
5. R. Beroukhim et al., Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma. Proc Natl Acad Sci 104, 20007-20012 (2007).
6. L. Ding et al., Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069-1075 (2008).
7. S. Jones et al., Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801-1806 (2008).
8. B. Vogelstein and K. W. Kinzler, Cancer genes and the pathways they control. Nat Med 10, 789-799 (2004).
9. D. Hanahan and R. A. Weinberg, Hallmarks of cancer: The next generation. Cell 144, 646-674 (2011).
10. S. M. Boca et al., Patient-oriented gene set analysis for cancer mutation data. Genome Biol 11, R112 (2010).
11. S. Efroni et al., Detecting cancer gene networks characterized by recurrent genomic alterations in a population. PLoS ONE 6, e14437 (2011).
12. F. Vandin, E. Upfal and B. J. Raphael, De novo discovery of mutated driver pathways in cancer. Genome Res 22, 375-385 (2012).
13. J. Zhao, S. Zhang, L. Y. Wu and X. S. Zhang. Efficient methods for identifying mutated driver pathways in cancer. In submission (2012).
14. E. Cerami et al., Automated network analysis identifies core pathways in glioblastoma. PLoS One 5, e8918 (2010).
15. G. Ciriello et al., Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 22, 398-406 (2012).
16. M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28, 27-30 (2000).
17. G. Joshi-Tope et al., Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33(suppl 1): D428-432 (2005).
18. C. A. Miller et al., Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Med Genomics 4, 34 (2011).
19. T. Ideker, O. Ozier, B. Schwikowski and A. F. Siegel, Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18(Suppl 1), S233-240 (2002).
20. E. Segal, H. Wang and D. Koller, Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 19(Suppl 1), i264-272 (2003).
21. D. L. Masica and R. Karchin, Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Res 71, 4550-4561 (2011).
22. G. W. Roel et al., Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98-110 (2010).
23. Y. Wang and Y. Xia, Condition specific subnetwork identification using an optimization model. Proceedings of the second international symposium on Optimization and Systems Biology (OSB'08), 333-340 (2008).
24. Y. Ye, A new complexity result on minimization of a quadratic function with a sphere constraint. in Recent advances in global optimization, New York: Princeton University Press Princeton, 19-31 (1992).
25. R. Tibshirani, Regression shrinkage and selection via the lasso. Journal of the Royal Statistical Society, Series B 58, 267-288 (1996).
26. R. G. Verhaak et al., Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98-110 (2010).
27. M. Mizoguchi et al., Genetic alterations of phosphoinositide 3-kinase subunit genes in human glioblastomas. Brain Pathol 14, 372-377 (2004).
28. L. M. Chow et al., Cooperativity within and among Pten, p53, and Rb pathways induces high-grade astrocytoma in adult brain. Cancer Cell 19, 305-316 (2011).
29. H. Zheng et al., p53 and Pten control neural and glioma stem/progenitor cell renewal and differentiation. Nature 455, 1129-1133 (2008).
30. Y. Zhu et al., Early inactivation of p53 tumor suppressor gene cooperating with NF1 loss induces malignant astrocytoma. Cancer Cell 8, 119-130 (2005).
31. M. Nakamura et al., Promoter hypermethylation of the RB1 gene in glioblastomas. Lab Invest 81, 77-82 (2001).
32. W. Y. Cheng et al., A Multi-Cancer Mesenchymal Transition Gene Expression Signature Is Associated with Prolonged Time to Recurrence in Glioblastoma. PLoS ONE 7, e34705 (2012).
33. H. W. Yang et al., SNAI2/Slug promotes growth and invasion in human gliomas. BMC Cancer 10: 301 (2010).
34. Y. Liu et al., Vascular gene expression patterns are conserved in primary and metastatic brain tumors. J Neurooncol 99, 13-24 (2000).
35. C. L. Tso et al., Distinct Transcription Profiles of Primary and Secondary Glioblastoma Subgroups. Cancer Res 66, 159-167 (2006).
36. X. L. Xu and A. M. Kapoun, Heterogeneous activation of the TGF pathway in glioblastomas identified by gene expression-based classification using TGF-responsive genes. Journal of Translational Medicine 7: 12 (2009).
37. P. Stephens et al., Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature 431, 525-526 (2004).
38. Y. Samuels et al., High frequency of mutations of the PIK3CA gene in human cancers. Science 304, 554 (2004).
39. G. L. Gallia et al., PIK3CA gene mutations in pediatric and adult glioblastoma multiforme. Mol Cancer Res 4, 709-714 (2006).
40. Entrez Gene: DST dystonin.
41. N. VL Seräo et al., Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival. BMC Medical Genomics 4: 49 (2011).
42. H. Dong et al., Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma. BMC Systems Biology 4: 163 (2010).
43. F. M. Hofman et al., Immunotherapy of Malignant Gliomas Using Autologous and Allogeneic Tissue Cells. Anti-Cancer Agents in Medicinal Chemistry 10, 462-470 (2010).