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Volumn 2013, Issue 1, 2013, Pages

Bayesian methods for expression-based integration of various types of genomics data Computational methods for biomarker discovery and systems biology research

Author keywords

Bayesian modeling; Genomics; Hierarchical models; Integrative analysis; Shrinkage priors

Indexed keywords

BAYESIAN NETWORKS; HIERARCHICAL SYSTEMS; SHRINKAGE;

EID: 84887049272     PISSN: 16874145     EISSN: 16874153     Source Type: Journal    
DOI: 10.1186/1687-4153-2013-13     Document Type: Article
Times cited : (22)

References (41)
  • 2
    • 84877838807 scopus 로고    scopus 로고
    • [Memorial Sloan-Kettering Cancer Center]. Accessed 9 August 2012
    • Pathway analysis of genetic alterations in glioblastoma (TCGA) http://cbio.mskcc.org/cancergenomics/gbm/pathways/ 2012. [Memorial Sloan-Kettering Cancer Center]. Accessed 9 August 2012.
    • (2012) Pathway Analysis of Genetic Alterations in Glioblastoma (TCGA)
  • 3
    • 84881317451 scopus 로고    scopus 로고
    • [The Cancer Genome Atlas]. Accessed 9 August 2012
    • Program overview http://cancergenome.nih.gov/abouttcga/overview 2012. [The Cancer Genome Atlas]. Accessed 9 August 2012
    • Program Overview
  • 4
    • 84872555791 scopus 로고    scopus 로고
    • IBAG: Integrative Bayesian analysis of high-dimensional multiplatform genomics data
    • 10.1093/bioinformatics/bts655
    • Wang W, Baladandayuthapani V, Morris JS, Broom BM, Manyam G, Do KA: iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data. Bioinformatics 2013,29(2):149-159.
    • (2013) Bioinformatics , vol.29 , Issue.2 , pp. 149-159
    • Wang, W.1    Baladandayuthapani, V.2    Morris, J.S.3    Broom, B.M.4    Manyam, G.5    Do, K.A.6
  • 7
    • 70449331456 scopus 로고    scopus 로고
    • Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    • 10.1093/bioinformatics/btp543
    • Shen R, Olshen AB, Ladanyi M: Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 2009,25(22):2906-2912.
    • (2009) Bioinformatics , vol.25 , Issue.22 , pp. 2906-2912
    • Shen, R.1    Olshen, A.B.2    Ladanyi, M.3
  • 8
    • 80054741545 scopus 로고    scopus 로고
    • Integrating diverse genomic data using gene sets
    • 10.1186/gb-2011-12-10-r105
    • Tyekucheva S, Marchionni L, Karchin R, Parmigiani G: Integrating diverse genomic data using gene sets. Genome Biol 2011,12(10):R105.
    • (2011) Genome Biol , vol.12 , Issue.10 , pp. 105
    • Tyekucheva, S.1    Marchionni, L.2    Karchin, R.3    Parmigiani, G.4
  • 9
  • 10
    • 36749013671 scopus 로고    scopus 로고
    • Semiparametric regression of multidimensional genetic pathway data: Least-squares kernel machines and linear mixed models
    • DOI 10.1111/j.1541-0420.2007.00799.x
    • Liu D, Lin X, Ghosh D: Semiparametric regression of multi-dimensional genetic pathway data: least squares kernel machines and linear mixed models. Biometrics 2007, 63:1079-1088. (Pubitemid 350212565)
    • (2007) Biometrics , vol.63 , Issue.4 , pp. 1079-1088
    • Liu, D.1    Lin, X.2    Ghosh, D.3
  • 11
    • 78650337471 scopus 로고    scopus 로고
    • Inference with normal-gamma prior distributions in regression problems
    • 2596440 10.1214/10-BA507
    • Griffin JE, Brown PJ: Inference with normal-gamma prior distributions in regression problems. Bayesian Anal 2010, 5:171-188.
    • (2010) Bayesian Anal , vol.5 , pp. 171-188
    • Griffin, J.E.1    Brown, P.J.2
  • 12
    • 0027080802 scopus 로고
    • The accelerated failure time model: A useful alternative to the Cox regression model in survival analysis
    • Wei LJ: The accelerated failure time model: A useful alternative to the cox regression model in survival analysis. Stat Med 1992,11(14-15):1871-1879. [ http://dx.doi.org/10.1002/sim.4780111409 ]. (Pubitemid 23015636)
    • (1992) Statistics in Medicine , vol.11 , Issue.14-15 , pp. 1871-1879
    • Wei, L.J.1
  • 13
    • 49549105778 scopus 로고    scopus 로고
    • The Bayesian lasso
    • 2524001 10.1198/016214508000000337
    • Park T, Casella G: The Bayesian lasso. J Am. Stat. Assoc 2008,103(482):681-686.
    • (2008) J Am. Stat. Assoc , vol.103 , Issue.482 , pp. 681-686
    • Park, T.1    Casella, G.2
  • 14
  • 15
    • 84861646034 scopus 로고    scopus 로고
    • Structuring shrinkage: Some correlated priors for regression
    • 2931267 10.1093/biomet/asr082 [ ]
    • Griffin JE, Brown PJ: Structuring shrinkage: some correlated priors for regression. Biometrika 2012,99(2):481-487. [ http://EconPapers.repec.org/RePEc: oup:biomet:v:99:y:2012:i:2:p:481-487 ].
    • (2012) Biometrika , vol.99 , Issue.2 , pp. 481-487
    • Griffin, J.E.1    Brown, P.J.2
  • 16
    • 4043135554 scopus 로고    scopus 로고
    • Optimal predictive model selection
    • DOI 10.1214/009053604000000238
    • Barbieri MM, Berger JO: Optimal predictive model selection. Ann. Stat 2004,32(3):870-897. (Pubitemid 41250287)
    • (2004) Annals of Statistics , vol.32 , Issue.3 , pp. 870-897
    • Barbieri, M.M.1    Berger, J.O.2
  • 18
    • 84887074666 scopus 로고    scopus 로고
    • 2013. [American Brain Tumor Association]. Accessed 6 June 2013
    • Glioblastoma http://www.abta.org/understanding-brain-tumors/types-of- tumors/glioblastoma.html 2013. [American Brain Tumor Association]. Accessed 6 June 2013
    • Glioblastoma
  • 19
    • 84863562673 scopus 로고    scopus 로고
    • Glioblastoma survival in the United States before and during the temozolomide era
    • 10.1007/s11060-011-0749-4
    • Johnson DR, O'Neill BP: Glioblastoma survival in the United States before and during the temozolomide era. J. Neurooncol 2012,107(2):359-364.
    • (2012) J. Neurooncol , vol.107 , Issue.2 , pp. 359-364
    • Johnson, D.R.1    O'Neill, B.P.2
  • 22
    • 84887100688 scopus 로고    scopus 로고
    • [TCGA]. Accessed 22 August 2013
    • Data levels and data types https://tcga-data.nci.nih.gov/tcga/ tcgaDataType.jsp. [TCGA]. Accessed 22 August 2013
    • Data Levels and Data Types
  • 24
    • 84895057195 scopus 로고    scopus 로고
    • FGF Receptors: Cancer Biology and Therapeutics
    • doi:10.1002/med.21288
    • Katoh M, Nakagama H: FGF Receptors: Cancer Biology and Therapeutics. Rev. Med. Res 2013. doi:10.1002/med.21288
    • (2013) Rev. Med. Res
    • Katoh, M.1    Nakagama, H.2
  • 25
    • 34848916733 scopus 로고    scopus 로고
    • FGFR1 over-expression in primary rhabdomyosarcoma tumors is associated with hypomethylation of a 5′ CpG island and abnormal expression of the AKT1, NOG, and BMP4 genes
    • DOI 10.1002/gcc.20489
    • Goldstein M, Meller I, Orr-Urtreger A: FGFR1 over-expression in primary rhabdomyosarcoma tumors is associated with hypomethylation of a 5' CpG island and abnormal expression of the AKT1, NOG, and BMP4 genes. Genes Chromosomes Cancer 2007,46(11):1028-1038. (Pubitemid 47502842)
    • (2007) Genes Chromosomes and Cancer , vol.46 , Issue.11 , pp. 1028-1038
    • Goldstein, M.1    Meller, I.2    Orr-Urtreger, A.3
  • 27
    • 0036141447 scopus 로고    scopus 로고
    • Insulin-like growth factor receptor I mediates resistance to anti-epidermal growth factor receptor therapy in primary human glioblastoma cells through continued activation of phosphoinositide 3-kinase signaling
    • Chakravarti A, Loeffler JS, Dyson NJ: Insulin-like growth factor receptor I mediates resistance to anti-epidermal growth factor receptor therapy in primary human glioblastoma cells through continued activation of phosphoinositide 3-kinase signaling. Cancer Res 2002, 62:200-207. (Pubitemid 34074005)
    • (2002) Cancer Research , vol.62 , Issue.1 , pp. 200-207
    • Chakravarti, A.1    Loeffler, J.S.2    Dyson, N.J.3
  • 28
    • 62749203737 scopus 로고    scopus 로고
    • Insulin-like growth factor 1 receptor targeted therapeutics: Novel compounds and novel treatment strategies for cancer medicine
    • 10.2174/157489209787002515
    • Hewish M, Chau I, Cunningham D: Insulin-like growth factor 1 receptor targeted therapeutics: novel compounds and novel treatment strategies for cancer medicine. Recent Pat. Anticancer Drug Discov 2009, 4:54-72.
    • (2009) Recent Pat. Anticancer Drug Discov , vol.4 , pp. 54-72
    • Hewish, M.1    Chau, I.2    Cunningham, D.3
  • 31
    • 84879695087 scopus 로고    scopus 로고
    • ARAF acts as a scaffold to stabilize BRAF: CRAF heterodimers
    • 10.1038/onc.2012.330
    • Rebocho AP, Marais R: ARAF acts as a scaffold to stabilize BRAF: CRAF heterodimers. Oncogene 2013,32(26):3207-3212.
    • (2013) Oncogene , vol.32 , Issue.26 , pp. 3207-3212
    • Rebocho, A.P.1    Marais, R.2
  • 34
    • 77954953329 scopus 로고    scopus 로고
    • SIRPalpha1 receptors interfere with the EGFRvIII signalosome to inhibit glioblastoma cell transformation and migration
    • 10.1038/onc.2010.164
    • Kapoor GS, O'Rourke DM: SIRPalpha1 receptors interfere with the EGFRvIII signalosome to inhibit glioblastoma cell transformation and migration. Oncogene 2010,29(29):4130-4144.
    • (2010) Oncogene , vol.29 , Issue.29 , pp. 4130-4144
    • Kapoor, G.S.1    O'Rourke, D.M.2
  • 35
    • 0029815093 scopus 로고    scopus 로고
    • Enhanced tumorigenic behavior of glioblastoma cells expressing a truncated epidermal growth factor receptor is mediated through the Ras-Shc- Grb2 pathway
    • DOI 10.1074/jbc.271.41.25639
    • Prigent SA, Nagane M, Lin H, Huvar I, Boss GR, Feramisco JR, Cavenee WK, Huang HS: Enhanced tumorigenic behavior of glioblastoma cells expressing a truncated epidermal growth factor receptor is mediated through the Ras-Shc-Grb2 pathway. J. Biol. Chem 1996,271(41):25639-25645. (Pubitemid 26337944)
    • (1996) Journal of Biological Chemistry , vol.271 , Issue.41 , pp. 25639-25645
    • Prigent, S.A.1    Nagane, M.2    Lin, H.3    Huvar, I.4    Boss, G.R.5    Feramisco, J.R.6    Cavenee, W.K.7    Su Huang, H.-J.8
  • 39
    • 79958098183 scopus 로고    scopus 로고
    • PDGF-B Can sustain self-renewal and tumorigenicity of experimental glioma-derived cancer-initiating cells by preventing oligodendrocyte differentiation
    • Jiang Y, Boije M, Westermark B, Uhrbom L: PDGF-B Can sustain self-renewal and tumorigenicity of experimental glioma-derived cancer-initiating cells by preventing oligodendrocyte differentiation. Neoplasia 2011,13(6):492-503.
    • (2011) Neoplasia , vol.13 , Issue.6 , pp. 492-503
    • Jiang, Y.1    Boije, M.2    Westermark, B.3    Uhrbom, L.4
  • 40
    • 77958527996 scopus 로고    scopus 로고
    • The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas
    • 10.1371/journal.pone.0012548
    • Cooper LA, Gutman DA, Long Q, Johnson BA, Cholleti SR, Kurc T, Saltz JH, Brat DJ, Moreno CS: The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas. PLoS ONE 2010,5(9):e12548.
    • (2010) PLoS ONE , vol.5 , Issue.9 , pp. 12548
    • Cooper, L.A.1    Gutman, D.A.2    Long, Q.3    Johnson, B.A.4    Cholleti, S.R.5    Kurc, T.6    Saltz, J.H.7    Brat, D.J.8    Moreno, C.S.9
  • 41
    • 70849122697 scopus 로고    scopus 로고
    • Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations
    • 10.1371/journal.pone.0007752
    • Brennan C, Momota H, Hambardzumyan D, Ozawa T, Tandon A, Pedraza A, Holland E: Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations. PLoS ONE 2009,4(11):e7752.
    • (2009) PLoS ONE , vol.4 , Issue.11 , pp. 7752
    • Brennan, C.1    Momota, H.2    Hambardzumyan, D.3    Ozawa, T.4    Tandon, A.5    Pedraza, A.6    Holland, E.7


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