Combined gene expression and protein interaction analysis of dynamic modularity in glioma prognosis

Journal of Neuro-Oncology

Volumn 107, Issue 2, 2012, Pages 281-288

  Zhang, Xiaoyu ^a   Yang, Hongbin ^a   Gong, Binsheng ^a   Jiang, Chuanlu ^a   Yang, Lizhuang ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Dynamic; Glioma; Modularity; Prognosis

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; MYC PROTEIN; RETINOBLASTOMA 1 PROTEIN; RETINOBLASTOMA PROTEIN; SYNAPTOPHYSIN; TRANSCRIPTION FACTOR E2F1; UNCLASSIFIED DRUG; BIOLOGICAL MARKER;

ACCURACY; ARTICLE; CANCER PROGNOSIS; CANCER SURVIVAL; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GLIOMA; HUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; SURVIVAL TIME; UPREGULATION; BIOLOGICAL MODEL; BIOLOGY; BRAIN TUMOR; METABOLISM; NONLINEAR SYSTEM; PHYSIOLOGY; PROGNOSIS;

BIOLOGICAL MARKERS; BRAIN NEOPLASMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GLIOMA; HUMANS; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; PROGNOSIS; PROTEIN INTERACTION MAPPING;

EID: 84863596942     PISSN: 0167594X     EISSN: 15737373     Source Type: Journal    
DOI: 10.1007/s11060-011-0757-4     Document Type: Article

References (32)

1. Rainov NG, Dobberstein KU, Bahn H, Holzhausen HJ, Lautenschlager C, Heidecke V, Burkert W (1997) Prognostic factors in malignant glioma: influence of the overexpression of oncogene and tumor-suppressor gene products on survival. J Neurooncol 35:13-28
2. Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL (2009) Dynamic modularity in protein-interaction networks predicts breast cancer outcome. Nat Biotechnol 27:199-204. doi:10.1038/nbt.1522
3. Yang J, Liao D, Wang Z, Liu F, Wu G (2011) Mammalian target of rapamycin signaling pathway contributes to glioma progression and patients' prognosis. J Surg Res 168:97-102. doi: 10.1016/j.jss.2009.06.025
4. Liu X, Tang H, Zhang Z, Li W, Wang Z, Zheng Y, Wu M, Li G (2011) POTEH hypomethylation, a new epigenetic biomarker for glioma prognosis. Brain Res 1391:125-131. doi:10.1016/j. brainres.2011.03.042
5. Wang C, Cao S, Yan Y, Ying Q, Jiang T, Xu K, Wu A (2010) TLR9 expression in glioma tissues correlated to glioma progression and the prognosis of GBM patients. BMC Cancer 10:415. doi:10.1186/1471-2407-10-415
6. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804. doi:10.1126/science.10750902 98/5594/799[pii]
7. Watson MA, Perry A, Budhraja V, Hicks C, Shannon WD, Rich KM (2001) Gene expression profiling with oligonucleotide microarrays distinguishes World Health Organization grade of oligodendrogliomas. Cancer Res 61:1825-1829
8. Fuller GN, Hess KR, Rhee CH, Yung WK, Sawaya RA, Bruner JM, Zhang W (2002) Molecular classification of human diffuse gliomas by multidimensional scaling analysis of gene expression profiles parallels morphology-based classification, correlates with survival, and reveals clinically-relevant novel glioma subsets. Brain Pathol 12:108-116
9. Masica DL, Karchin R (2011) Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Res 71:4550-4561. doi:10. 1158/0008-5472.CAN-11-0180
10. Boudreau CR, Yang I, Liau LM (2005) Gliomas: advances in molecular analysis and characterization. Surg Neurol 64:286-294; discussion 294
11. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, Misra A, Nigro JM, Colman H, Soroceanu L, Williams PM, Modrusan Z, Feuerstein BG, Aldape K (2006) Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 9:157-173. doi:10.1016/j.ccr.2006.02.019
12. Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21:2076-2082. doi:10.1093/bioinformatics/bti273
13. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15
14. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006) Single-cell proteomic analysis of S. Cerevisiae reveals the architecture of biological noise. Nature 441:840-846. doi:10.1038/nature04785
15. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98:5116-5121. doi:10.1073/pnas.091062498
16. Larsson O, Wahlestedt C, Timmons JA (2005) Considerations when using the significance analysis of microarrays (SAM) algorithm. BMC Bioinformatics 6:129. doi:10.1186/14712105-6-129
17. Jin R, McCallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ (2009) Identifying dynamic network modules with temporal and spatial constraints. Pac Symp Biocomput: 203-214
18. Suzuki H (2006) Protein-protein interactions in the mammalian brain. J Physiol 575:373-377. doi:10.1113/jphysiol.2006.115717
19. Yao C, Li H, Zhou C, Zhang L, Zou J, Guo Z (2010) Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. BMC Syst Biol 4:151. doi:10.1186/17520509-4-151
20. Sano M, Genkai N, Yajima N, Tsuchiya N, Homma J, Tanaka R, Miki T, Yamanaka R (2006) Expression level of ECT2 protooncogene correlates with prognosis in glioma patients. Oncol Rep 16:1093-1098
21. Genkai N, Homma J, Sano M, Tanaka R, Yamanaka R (2006) Increased expression of pituitary tumor-transforming gene (PTTG)-1 is correlated with poor prognosis in glioma patients. Oncol Rep 15:1569-1574
22. Sun B, Chu D, Li W, Chu X, Li Y, Wei D, Li H (2009) Decreased expression of NDRG1 in glioma is related to tumor progression and survival of patients. J Neurooncol 94:213-219. doi:10.1007/s11060-009-9859-7
23. Wang Y, Weil BR, Herrmann JL, Abarbanell AM, Tan J, Markel TA, Kelly ML, Meldrum DR (2009) MEK, p38, and PI-3K mediate cross talk between EGFR and TNFR in enhancing hepatocyte growth factor production from human mesenchymal stem cells. Am J Physiol Cell Physiol 297:C1284-C1293. doi: 10.1152/ajpcell.00183. 2009
24. De Carli E, Wang X, Puget S (2009) IDH1 and IDH2 mutations in gliomas. N Engl J Med 360:2248; author reply 2249. doi: 10.1056/NEJMc090593
25. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, Kros JM, Hainfellner JA, Mason W, Mariani L, Bromberg JE, Hau P, Mirimanoff RO, Cairncross JG, Janzer RC, Stupp R (2005) MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 352:997-1003. doi: 10.1056/NEJMoa043331
26. Durand KS, Guillaudeau A, Weinbreck N, DeArmas R, Robert S, Chaunavel A, Pommepuy I, Bourthoumieu S, Caire F, Sturtz FG, Labrousse FJ (2010) 1p19q LOH patterns and expression of p53 and Olig2 in gliomas: relation with histological types and prognosis. Mod Pathol 23:619-628. doi:10.1038/modpathol.2009.185
27. Crowe DL, Nguyen DC (2001) Rb and E2F-1 regulate telomerase activity in human cancer cells. Biochim Biophys Acta 1518:1-6. doi:10.1016/S0167-4781(00) 00296-7
28. Xu K, Shu HK (2007) EGFR activation results in enhanced cyclooxygenase-2 expression through p38 mitogen-activated protein kinase-dependent activation of the Sp1/Sp3 transcription factors in human gliomas. Cancer Res 67:6121-6129. doi: 10.1158/0008-5472.CAN-07-0141
29. Ventura JJ, Tenbaum S, Perdiguero E, Huth M, Guerra C, Barbacid M, Pasparakis M, Nebreda AR (2007) p38alpha MAP kinase is essential in lung stem and progenitor cell proliferation and differentiation. Nat Genet 39:750-758. doi:10.1038/ng2037
30. Bodnar AG, Ouellette M, Frolkis M, Holt SE, Chiu CP, Morin GB, Harley CB, Shay JW, Lichtsteiner S, Wright WE (1998) Extension of life-span by introduction of telomerase into normal human cells. Science 279:349-352
31. Kanaya T, Kyo S, Hamada K, Takakura M, Kitagawa Y, Harada H, Inoue M (2000) Adenoviral expression of p53 represses telomerase activity through down-regulation of human telomerase reverse transcriptase transcription. Clin Cancer Res 6:1239-1247
32. Chandra H, Reddy PJ, Srivastava S (2011) Protein microarrays and novel detection platforms. Expert Rev Proteomics 8:61-79. doi:10.1586/epr.10.99