메뉴 건너뛰기




Volumn 7, Issue , 2011, Pages

Network modeling of the transcriptional effects of copy number aberrations in glioblastoma

Author keywords

cancer biology; cancer genomics; glioblastoma

Indexed keywords

1 TERT BUTYL 3 [6 (3,5 DIMETHOXYPHENYL) 2 (4 DIETHYLAMINOBUTYLAMINO)PYRIDO[2,3 D]PYRIMIDIN 7 YL]UREA; 5 (4 CHLOROPHENYL) 1 (4 METHOXYPHENYL) 3 TRIFLUOROMETHYL 1H PYRAZOLE; ANTINEOPLASTIC AGENT; ENURACIL; FORMYCIN; GEFITINIB; GENOMIC DNA; GENOMIC RNA; IMATINIB; JTT 130; KI 23057; LY 333013; MEPYRAMINE; MESSENGER RNA; NECDIN; ONCOPROTEIN; PROTEIN HUB; SDX 102; SIMVASTATIN; SUNITINIB; UNCLASSIFIED DRUG; VOGLIBOSE; NERVE PROTEIN; NUCLEAR PROTEIN; PROTEIN P53;

EID: 79955562657     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.17     Document Type: Article
Times cited : (75)

References (73)
  • 7
    • 0030344230 scopus 로고    scopus 로고
    • Heuristics of instability and stabilization in model selection
    • Breiman L (1996) Heuristics of instability and stabilization in model selection. Ann Statist 24: 2350-2383
    • (1996) Ann Statist , vol.24 , pp. 2350-2383
    • Breiman, L.1
  • 10
    • 77949446630 scopus 로고    scopus 로고
    • Automated network analysis identifies core pathways in glioblastoma
    • Cerami E, Demir E, Schultz N, Taylor BS, Sander C (2010) Automated network analysis identifies core pathways in glioblastoma. PLoS ONE 5: e8918
    • (2010) PLoS ONE , vol.5
    • Cerami, E.1    Demir, E.2    Schultz, N.3    Taylor, B.S.4    Sander, C.5
  • 11
    • 3142617691 scopus 로고    scopus 로고
    • Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
    • DOI 10.1016/j.pbiomolbio.2004.04.002, PII S007961070400046X
    • Crampin EJ, Schnell S, McSharry PE (2004) Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog Biophys Mol Biol 86: 77-112 (Pubitemid 38946555)
    • (2004) Progress in Biophysics and Molecular Biology , vol.86 , Issue.1 , pp. 77-112
    • Crampin, E.J.1    Schnell, S.2    McSharry, P.E.3
  • 12
    • 70349330124 scopus 로고    scopus 로고
    • Genomic aberrations in 80 cases of primary glioblastoma multiforme: Pathogenetic heterogeneity and putative cytogenetic pathways
    • Dahlback HSS, Brandal P, Meling TR, Gorunova L, Scheie D, Heim S (2009) Genomic aberrations in 80 cases of primary glioblastoma multiforme: pathogenetic heterogeneity and putative cytogenetic pathways. Genes Chromosomes Cancer 48: 908-924
    • (2009) Genes Chromosomes Cancer , vol.48 , pp. 908-924
    • Hss, D.1    Brandal, P.2    Meling, T.R.3    Gorunova, L.4    Scheie, D.5    Heim, S.6
  • 13
    • 0035425048 scopus 로고    scopus 로고
    • PDGF autocrine stimulation dedifferentiates cultured astrocytes and induces oligodendrogliomas from and oligoastrocytomas neural progenitors and astrocytes in vivo
    • DOI 10.1101/gad.903001
    • Dai C, Celestino JC, Okada Y, Louis DN, Fuller GN, Holland EC (2001) PDGF autocrine stimulation dedifferentiates cultured astrocytes and induces oligodendrogliomas and oligoastrocytomas from neural progenitors and astrocytes in vivo. Genes Dev 15: 1913-1925 (Pubitemid 32738621)
    • (2001) Genes and Development , vol.15 , Issue.15 , pp. 1913-1925
    • Dai, C.1    Celestino, J.C.2    Okada, Y.3    Louis, D.N.4    Fuller, G.N.5    Holland, E.C.6
  • 15
    • 33748041449 scopus 로고    scopus 로고
    • Autocrine/paracrine platelet-derived growth factor regulates proliferation of neural progenitor cells
    • DOI 10.1158/0008-5472.CAN-06-0900
    • Erlandsson A, Brännvall K, Gustafsdottir S, Westermark B, Forsberg-Nilsson K (2006) Autocrine/paracrine platelet-derived growth factor regulates proliferation of neural progenitor cells. Cancer Res 66: 8042-8048 (Pubitemid 44299169)
    • (2006) Cancer Research , vol.66 , Issue.16 , pp. 8042-8048
    • Erlandsson, A.1    Brannvall, K.2    Gustafsdottir, S.3    Westermark, B.4    Forsberg-Nilsson, K.5
  • 19
  • 20
    • 0032361278 scopus 로고    scopus 로고
    • Penalized regressions: The bridge versus the lasso
    • Fu WJ (1998) Penalized regressions: the bridge versus the lasso. J Comput Graph Statist 7: 397-416
    • (1998) J Comput Graph Statist , vol.7 , pp. 397-416
    • Fu, W.J.1
  • 22
    • 0004236492 scopus 로고    scopus 로고
    • Baltimore, MD, USA: Johns Hopkins University Press
    • Golub GH, Loan CFV (1996) Matrix computations. Baltimore, MD, USA: Johns Hopkins University Press
    • (1996) Matrix Computations
    • Golub, G.H.1    Cfv, L.2
  • 23
    • 66449094631 scopus 로고    scopus 로고
    • Expression of Sox11 in adult neurogenic niches suggests a stage-specific role in adult neurogenesis
    • Haslinger A, Schwarz TJ, Covic M, Lie DC (2009) Expression of Sox11 in adult neurogenic niches suggests a stage-specific role in adult neurogenesis. Eur J Neurosci 29: 2103-2114
    • (2009) Eur J Neurosci , vol.29 , pp. 2103-2114
    • Haslinger, A.1    Schwarz, T.J.2    Covic, M.3    Lie, D.C.4
  • 24
    • 0037306536 scopus 로고    scopus 로고
    • Studying complex biological systems using multifactorial perturbation
    • DOI 10.1038/nrg996
    • Jansen RC (2003) Studying complex biological systems using multifactorial perturbation. Nat Rev Genet 4: 145-151 (Pubitemid 36150686)
    • (2003) Nature Reviews Genetics , vol.4 , Issue.2 , pp. 145-151
    • Jansen, R.C.1
  • 25
    • 0029022716 scopus 로고
    • Multiple trait analysis of genetic mapping for quantitative trait loci
    • Jiang C, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127
    • (1995) Genetics , vol.140 , pp. 1111-1127
    • Jiang, C.1    Zeng, Z.B.2
  • 26
    • 84976789814 scopus 로고
    • Efficient algorithms for shortest paths in sparse networks
    • Johnson D (1977) Efficient algorithms for shortest paths in sparse networks. J Acm24: 1-13
    • (1977) J Acm , vol.24 , pp. 1-13
    • Johnson, D.1
  • 28
    • 78650267786 scopus 로고    scopus 로고
    • Simultaneous identification of causal genes and Dys-regulated pathways in complex disease
    • Kim YA,Wuchty S, Przytycka TM(2010) Simultaneous identification of causal genes and Dys-regulated pathways in complex disease. Res Comput Mol Biol (RECOMB) 6044: 263-280
    • (2010) Res Comput Mol Biol (RECOMB) , vol.6044 , pp. 263-280
    • Kim, Y.A.1    Wuchty, S.2    Przytycka, T.M.3
  • 29
    • 62749120322 scopus 로고    scopus 로고
    • A phase II multicenter study of L-alanosine, a potent inhibitor of adenine biosynthesis, in patients with MTAP-deficient cancer
    • Kindler HL, Burris HA, Sandler AB, Oliff IA (2009) A phase II multicenter study of L-alanosine, a potent inhibitor of adenine biosynthesis, in patients with MTAP-deficient cancer. Invest New Drugs 27: 75-81
    • (2009) Invest New Drugs , vol.27 , pp. 75-81
    • Kindler, H.L.1    Burris, H.A.2    Sandler, A.B.3    Oliff, I.A.4
  • 30
    • 63849145908 scopus 로고    scopus 로고
    • NIRest: A tool for gene network and mode of action inference
    • Lauria M, Iorio F, di Bernardo D (2009) NIRest: a tool for gene network and mode of action inference. Ann N Y Acad Sci 1158: 257-264
    • (2009) Ann N y Acad Sci , vol.1158 , pp. 257-264
    • Lauria, M.1    Iorio, F.2    Di Bernardo, D.3
  • 31
    • 41349122898 scopus 로고    scopus 로고
    • Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
    • DOI 10.1093/bioinformatics/btn034
    • Lee H, Kong SW, Park PJ (2008) Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics 24: 889-896 (Pubitemid 351448021)
    • (2008) Bioinformatics , vol.24 , Issue.7 , pp. 889-896
    • Lee, H.1    Kong, S.W.2    Park, P.J.3
  • 36
    • 77954576424 scopus 로고    scopus 로고
    • Revealing ecological networks using Bayesian network inference algorithms
    • Milns I, Beale CM, Smith VA (2010) Revealing ecological networks using Bayesian network inference algorithms. Ecology 91: 1892-1899
    • (2010) Ecology , vol.91 , pp. 1892-1899
    • Milns, I.1    Beale, C.M.2    Smith, V.A.3
  • 38
    • 0036956225 scopus 로고    scopus 로고
    • Partial least squares proportional hazard regression for application to DNA microarray survival data
    • DOI 10.1093/bioinformatics/18.12.1625
    • Nguyen DV, Rocke DM (2002a) Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics 18: 1625-1632 (Pubitemid 36097728)
    • (2002) Bioinformatics , vol.18 , Issue.12 , pp. 1625-1632
    • Nguyen, D.V.1    Rocke, D.M.2
  • 39
    • 0036166439 scopus 로고    scopus 로고
    • Tumor classification by partial least squares using microarray gene expression data
    • Nguyen DV, Rocke DM (2002b) Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 18: 39-50 (Pubitemid 34145030)
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 39-50
    • Nguyen, D.V.1    Rocke, D.M.2
  • 40
    • 46249086537 scopus 로고    scopus 로고
    • An improved method for detecting and delineating genomic regions with altered gene expression in cancer
    • Nilsson B, Johansson M, Heyden A, Nelander S, Fioretos T (2008) An improved method for detecting and delineating genomic regions with altered gene expression in cancer. Genome Biol 9: R13
    • (2008) Genome Biol , vol.9
    • Nilsson, B.1    Johansson, M.2    Heyden, A.3    Nelander, S.4    Fioretos, T.5
  • 41
    • 70349548793 scopus 로고    scopus 로고
    • Interampatteness - A generic property of biochemical networks
    • Nordling TEM, Jacobsen EW (2009) Interampatteness - a generic property of biochemical networks. IET Syst Biol 3: 388-403
    • (2009) IET Syst Biol , vol.3 , pp. 388-403
    • Tem, N.1    Jacobsen, E.W.2
  • 42
    • 34848903220 scopus 로고    scopus 로고
    • From correlation to causation networks: A simple approximate learning algorithm and its application to high-dimensional plant gene expression data
    • Opgen-Rhein R, Opgen-Rhein and Strimmer K (2007) From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst Biol 1: 37
    • (2007) BMC Syst Biol , vol.1 , pp. 37
    • Opgen-Rhein, R.1    Opgen-Rhein2    Strimmer, K.3
  • 49
    • 57649124192 scopus 로고    scopus 로고
    • Reverse engineering the genotype-phenotype map with natural genetic variation
    • Rockman MV (2008) Reverse engineering the genotype-phenotype map with natural genetic variation. Nature 456: 738-744
    • (2008) Nature , vol.456 , pp. 738-744
    • Rockman, M.V.1
  • 50
    • 0014658880 scopus 로고
    • Biochemical systems analysis. II. The steadystate solutions for an n-pool system using a power-law approximation
    • Savageau MA (1969) Biochemical systems analysis. II. The steadystate solutions for an n-pool system using a power-law approximation. J Theor Biol 25: 370-379
    • (1969) J Theor Biol , vol.25 , pp. 370-379
    • Savageau, M.A.1
  • 52
    • 15944364151 scopus 로고    scopus 로고
    • An empirical Bayes approach to inferring large-scale gene association networks
    • DOI 10.1093/bioinformatics/bti062
    • Schäfer J, Strimmer K (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21: 754-764 (Pubitemid 40439411)
    • (2005) Bioinformatics , vol.21 , Issue.6 , pp. 754-764
    • Schafer, J.1    Strimmer, K.2
  • 58
    • 42949096140 scopus 로고    scopus 로고
    • EQED: An efficient method for interpreting eQTL associations using protein networks
    • Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol 4: 162
    • (2008) Mol Syst Biol , vol.4 , pp. 162
    • Suthram, S.1    Beyer, A.2    Karp, R.M.3    Eldar, Y.4    Ideker, T.5
  • 59
    • 0031964697 scopus 로고    scopus 로고
    • Necdin, a postmitotic neuron-specific growth suppressor, interacts with viral transforming proteins and cellular transcription factor E2F1
    • DOI 10.1074/jbc.273.2.720
    • Taniura H, Taniguchi N, Hara M, Yoshikawa K (1998) Necdin, a postmitotic neuron-specific growth suppressor, interacts with viral transforming proteins and cellular transcription factor E2F1. J Biol Chem 273: 720-728 (Pubitemid 28049158)
    • (1998) Journal of Biological Chemistry , vol.273 , Issue.2 , pp. 720-728
    • Taniura, H.1    Taniguchi, N.2    Hara, M.3    Yoshikawa, K.4
  • 61
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • TCGA-Consortium
    • TCGA-Consortium (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 64
    • 45849107285 scopus 로고    scopus 로고
    • Architecture of an antagonistic tree/fungus network: The asymmetric influence of past evolutionary history
    • Vacher C, Piou D, Desprez-Loustau ML (2008) Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history. PLoS ONE 3: e1740
    • (2008) PLoS ONE , vol.3
    • Vacher, C.1    Piou, D.2    Desprez-Loustau, M.L.3
  • 66
    • 38849098283 scopus 로고    scopus 로고
    • Quantifying the association between gene expressions and DNAmarkers by penalized canonical correlation analysis
    • Article3
    • Waaijenborg S, de Witt Hamer PCV, Zwinderman AH (2008) Quantifying the association between gene expressions and DNAmarkers by penalized canonical correlation analysis. Stat Appl Genet Mol Biol 7, Article3
    • (2008) Stat Appl Genet Mol Biol , vol.7
    • Waaijenborg, S.1    De Witt Hamer Pcv2    Zwinderman, A.H.3
  • 67
    • 70149096300 scopus 로고    scopus 로고
    • A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
    • Witten DM, Tibshirani R, Hastie T (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10: 515-534
    • (2009) Biostatistics , vol.10 , pp. 515-534
    • Witten, D.M.1    Tibshirani, R.2    Hastie, T.3
  • 71
    • 34247556038 scopus 로고    scopus 로고
    • Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations
    • Zhu J, Wiener MC, Zhang C, Fridman A, Minch E, Lum PY, Sachs JR, Schadt EE (2007) Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLoS Comput Biol 3: e69
    • (2007) PLoS Comput Biol , vol.3
    • Zhu, J.1    Wiener, M.C.2    Zhang, C.3    Fridman, A.4    Minch, E.5    Lum, P.Y.6    Sachs, J.R.7    Schadt, E.E.8
  • 72
    • 45149106353 scopus 로고    scopus 로고
    • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
    • DOI 10.1038/ng.167, PII NG167
    • Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 40: 854-861 (Pubitemid 351913653)
    • (2008) Nature Genetics , vol.40 , Issue.7 , pp. 854-861
    • Zhu, J.1    Zhang, B.2    Smith, E.N.3    Drees, B.4    Brem, R.B.5    Kruglyak, L.6    Bumgarner, R.E.7    Schadt, E.E.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.