메뉴 건너뛰기




Volumn 17, Issue 5-6, 2011, Pages 483-511

Probabilistic methods in cancer biology

Author keywords

Bayesian networks; Cancer biology; Data processing inequality; Markov chains; Mutual information; Page rank algorithm; Random walk; Statistical significance analysis

Indexed keywords

DATA HANDLING; DISEASES; GENE EXPRESSION; MARKOV PROCESSES; REVERSE ENGINEERING;

EID: 84055197830     PISSN: 09473580     EISSN: None     Source Type: Journal    
DOI: 10.3166/EJC.17.483-511     Document Type: Article
Times cited : (9)

References (67)
  • 1
    • 78649976005 scopus 로고    scopus 로고
    • An integrated approach to uncover drivers of cancer
    • Akavia UD, et al. An integrated approach to uncover drivers of cancer. Cell 2010; 143(6): 1005-1017.
    • (2010) Cell , vol.143 , Issue.6 , pp. 1005-1017
    • Akavia, U.D.1
  • 2
    • 79952108571 scopus 로고    scopus 로고
    • Inference of signal trans-duction networks from double causal evidence
    • Albert R, Dasgupta B, Sontag E. Inference of signal trans-duction networks from double causal evidence. Comput Biol 2010; 673: 239-251.
    • (2010) Comput Biol , vol.673 , pp. 239-251
    • Albert, R.1    Dasgupta, B.2    Sontag, E.3
  • 4
    • 0036100113 scopus 로고    scopus 로고
    • Context-specific Bayesian clustering for gene expression data
    • Barash Y, Friedman N. Context-specific Bayesian clustering for gene expression data. J Comput Biol 2002; 9(2): 169-191.
    • (2002) J Comput Biol , vol.9 , Issue.2 , pp. 169-191
    • Barash, Y.1    Friedman, N.2
  • 5
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and, function
    • Bartel D. MicroRNAs: Genomics, biogenesis, mechanism, and, function. Cell 2004; 116: 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.1
  • 6
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel D. MicroRNAs: Target recognition and regulatory functions. Cell 2009; 136: 219-236.
    • (2009) Cell , vol.136 , pp. 219-236
    • Bartel, D.1
  • 7
    • 16844376909 scopus 로고    scopus 로고
    • Reverse engineering of regulatory networks in human B cells
    • Basso K, et al. Reverse engineering of regulatory networks in human B cells. Nat Genetics 2005; 37(4): 382-390.
    • (2005) Nat Genetics , vol.37 , Issue.4 , pp. 382-390
    • Basso, K.1
  • 8
    • 0024376173 scopus 로고
    • Ras oncogenes in human cancer: A review
    • Bos JL. Ras oncogenes in human cancer: A review. Cancer Res 1989; 49(17): 4682-4689.
    • (1989) Cancer Res , vol.49 , Issue.17 , pp. 4682-4689
    • Bos, J.L.1
  • 9
    • 0038589165 scopus 로고    scopus 로고
    • The anatomy of a large-scale hypertextual web search engine
    • Brin S, Page L. The anatomy of a large-scale hypertextual web search engine. Comput Netw ISDN Syst 1998; 30(10): 107-117.
    • (1998) Comput Netw ISDN Syst , vol.30 , Issue.10 , pp. 107-117
    • Brin, S.1    Page, L.2
  • 10
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measures
    • Butte AJ, Kohane IS. Mutual information relevance networks: Functional genomic clustering using pairwise entropy measures. Pac, Sym Biocomputing 2000; 418-429.
    • (2000) Pac, Sym Biocomputing , pp. 418-429
    • Butte, A.J.1    Kohane, I.S.2
  • 11
    • 23444431611 scopus 로고
    • Green uorescent protein as a marker for gene expression
    • Chalife M, et al. Green uorescent protein as a marker for gene expression. Sci 1994; 263: 802-805.
    • (1994) Sci , vol.263 , pp. 802-805
    • Chalife, M.1
  • 12
    • 84933530882 scopus 로고
    • Approximating discrete probability distributions with dependence trees
    • Chow CK, Liu CN. Approximating discrete probability distributions with dependence trees. IEEE Trans Info Thy 1968; 14(3): 462-467.
    • (1968) IEEE Trans Info Thy , vol.14 , Issue.3 , pp. 462-467
    • Chow, C.K.1    Liu, C.N.2
  • 14
    • 84055213451 scopus 로고    scopus 로고
    • Reverse engineering of molecular networks from a common combinatorial approach
    • Eiloumi M, Zomaya AY, Eds.), Wiley, New York
    • Dasgupta B, Licona PV, Sontag E. Reverse engineering of molecular networks from a common combinatorial approach. In Algorithms in Computational Molecular Biology, (Eiloumi M, Zomaya AY, Eds.), Wiley, New York, 2011.
    • (2011) Algorithms In Computational Molecular Biology
    • Dasgupta, B.1    Licona, P.V.2    Sontag, E.3
  • 16
    • 77955484846 scopus 로고    scopus 로고
    • Identifying tightly regulated and variably expressed networks by differential rank conservation (DIRAC)
    • Eddy JA, et al. Identifying tightly regulated and variably expressed networks by differential rank conservation (DIRAC). PLOS Comput Biol 2010; 5(5).
    • (2010) PLOS Comput Biol , vol.5 , Issue.5
    • Eddy, J.A.1
  • 17
    • 35348890683 scopus 로고    scopus 로고
    • On testing the significance of a set of genes
    • Efron B, Tibshirani R. On testing the significance of a set of genes. Anna Appl Stat 2007; 1(1): 107-129.
    • (2007) Anna Appl Stat , vol.1 , Issue.1 , pp. 107-129
    • Efron, B.1    Tibshirani, R.2
  • 18
    • 79959895694 scopus 로고    scopus 로고
    • Functional parsing of driver mutations in the colorectal cancer genome reveals numerous suppressors of anchorage-independent growth
    • Eskiocak U, et al. Functional parsing of driver mutations in the colorectal cancer genome reveals numerous suppressors of anchorage-independent growth. Cancer Res 2011; 71: 4359-4365.
    • (2011) Cancer Res , vol.71 , pp. 4359-4365
    • Eskiocak, U.1
  • 20
    • 77955416779 scopus 로고    scopus 로고
    • Identification of regulatory network motifs from gene expression data
    • Farina L, et al. Identification of regulatory network motifs from gene expression data. J Math Model Algor 2010; 9(3): 233-245.
    • (2010) J Math Model Algor , vol.9 , Issue.3 , pp. 233-245
    • Farina, L.1
  • 21
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Friedman N. Inferring cellular networks using probabilistic graphical models. Sci 2004; 303: 799-805
    • (2004) Sci , vol.303 , pp. 799-805
    • Friedman, N.1
  • 22
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman N, et al. Using Bayesian networks to analyze expression data. J Comput Biol 2000; 7(3-4): 601-620.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1
  • 23
    • 33947101019 scopus 로고    scopus 로고
    • Patterns of somatic mutation in human cancer genomes
    • Greenman C, et al. Patterns of somatic mutation in human cancer genomes. Nat 2007; 132: 153-158.
    • (2007) Nat , vol.132 , pp. 153-158
    • Greenman, C.1
  • 24
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA targeting specificity in mammals: Determinants beyond seed pairing
    • Grimson A, et al. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell 2007; 27: 91-105.
    • (2007) Mol Cell , vol.27 , pp. 91-105
    • Grimson, A.1
  • 26
    • 85180872142 scopus 로고    scopus 로고
    • http://cancergenome.nih.gov
  • 27
    • 85180865907 scopus 로고    scopus 로고
    • http://seer.cancer.gov/statfacts/html/all.html
  • 28
    • 85180905039 scopus 로고    scopus 로고
    • http://www.medterms.com
  • 29
    • 85180914462 scopus 로고    scopus 로고
    • http://www.ncbi.nlm.nih.gov/geo/
  • 30
    • 85180894427 scopus 로고    scopus 로고
    • http://www.ncbi.nlm.nih.gov/unigene
  • 31
    • 85180830839 scopus 로고    scopus 로고
    • http://www.sanger.ac.uk/genetics/CGP/cosmic
  • 32
    • 85180872700 scopus 로고    scopus 로고
    • http://www.targetscan.org
  • 33
    • 85180903001 scopus 로고    scopus 로고
    • http://www.thefullwiki.org/Ancient Egyptian medicine
  • 34
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Research Consortium
    • International Human Genome Research Consortium. Initial sequencing and analysis of the human genome. Nat 2001; 409: 860-921.
    • (2001) Nat , vol.409 , pp. 860-921
  • 35
    • 77956541733 scopus 로고    scopus 로고
    • Distributed randomized algorithms for the page rank computation
    • Ishii H, Tempo R. Distributed randomized algorithms for the page rank computation. IEEE Trans Auto Control 2010; 55(9): 1897-2002.
    • (2010) IEEE Trans Auto Control , vol.55 , Issue.9 , pp. 1897-2002
    • Ishii, H.1    Tempo, R.2
  • 36
    • 0031572682 scopus 로고    scopus 로고
    • A multivariable Kolmogorov-Smirnov test of goodness of fit
    • Justel A, Peña D, Zamar R. A multivariable Kolmogorov-Smirnov test of goodness of fit. Stat Probab Lett 2007; 35: 251-259.
    • (2007) Stat Probab Lett , vol.35 , pp. 251-259
    • Justel, A.1    Peña, D.2    Zamar, R.3
  • 37
    • 54949085398 scopus 로고    scopus 로고
    • K-ras mutations and benefit from cetux-imab in advanced colorectal cancer
    • Karapetis CS, et al. K-ras mutations and benefit from cetux-imab in advanced colorectal cancer. New Engl J Med 2008; 359(17): 1757-1765.
    • (2008) New Engl J Med , vol.359 , Issue.17 , pp. 1757-1765
    • Karapetis, C.S.1
  • 39
    • 79551600768 scopus 로고    scopus 로고
    • Principal network analysis: Identification of subnetworks representing major dynamics using gene expression data
    • Kim Y, et al. Principal network analysis: Identification of subnetworks representing major dynamics using gene expression data. Bioinf 2011; 27(3): 391-398.
    • (2011) Bioinf , vol.27 , Issue.3 , pp. 391-398
    • Kim, Y.1
  • 40
    • 0030829782 scopus 로고    scopus 로고
    • K-Ras is essential for the development of the mouse embryo
    • Koera K, et al. K-Ras is essential for the development of the mouse embryo. Oncogene 1997; 15(10): 1151-1159.
    • (1997) Oncogene , vol.15 , Issue.10 , pp. 1151-1159
    • Koera, K.1
  • 41
    • 78049437880 scopus 로고    scopus 로고
    • Useofdata-biased random walks on graphs for the retrieval of context-specific networks from genomic data
    • Komurov K, White MA, Ram PT. Useofdata-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PLoS Computa-tional Biol 2010; 6(8): 19.
    • (2010) PLoS Computa-tional Biol , vol.6 , Issue.8 , pp. 19
    • Komurov, K.1    White, M.A.2    Ram, P.T.3
  • 42
    • 79951531878 scopus 로고    scopus 로고
    • From biological pathways to regulatory networks
    • Layek R, Datta A, Dougherty ER. From biological pathways to regulatory networks. Mol Biosys 2011; 7: 843-851.
    • (2011) Mol Biosys , vol.7 , pp. 843-851
    • Layek, R.1    Datta, A.2    Dougherty, E.R.3
  • 43
    • 79951539181 scopus 로고    scopus 로고
    • Cancer therapy design based on pathway logic
    • Layek R, et al. Cancer therapy design based on pathway logic. Bioinf 2011; 27(4): 548-555.
    • (2011) Bioinf , vol.27 , Issue.4 , pp. 548-555
    • Layek, R.1
  • 44
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often anked by adenosines, indicates that thous,s of human genes are microRNA targets
    • Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often anked by adenosines, indicates that thous,s of human genes are microRNA targets. Cell 2005; 120: 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 46
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a cellular context
    • Margolin AA, et al. ARACNE: An algorithm for the reconstruction of gene regulatory networks in a cellular context. BMC Bioinf 2008; 7(Supplement 1): S7.
    • (2008) BMC Bioinf , vol.7 , Issue.SUPPL. 1
    • Margolin, A.A.1
  • 49
    • 79952635505 scopus 로고    scopus 로고
    • Principles and strategies for developing network models in cancer
    • Pe'er D, Hacohen M. Principles and strategies for developing network models in cancer. Cell 2011; 144: 864-873.
    • (2011) Cell , vol.144 , pp. 864-873
    • Pe'er, D.1    Hacohen, M.2
  • 50
    • 20044363093 scopus 로고    scopus 로고
    • Replacement of K-Ras with H-Ras supports normal embryonic developmentdespite inducing cardiovascular pathology in adult mice
    • Potenza N, et al. Replacement of K-Ras with H-Ras supports normal embryonic developmentdespite inducing cardiovascular pathology in adult mice. EMBO Rep 2000; 6(5): 432-437.
    • (2000) EMBO Rep , vol.6 , Issue.5 , pp. 432-437
    • Potenza, N.1
  • 51
    • 77249113807 scopus 로고    scopus 로고
    • Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks
    • Qiu, P, Gentles AJ, Plevritis SK. Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks. J Comput Biol 2010; 17(2): 169-176.
    • (2010) J Comput Biol , vol.17 , Issue.2 , pp. 169-176
    • Qiu, P.1    Gentles, A.J.2    Plevritis, S.K.3
  • 53
    • 33749993417 scopus 로고    scopus 로고
    • The consensus coding sequences of human breast and colorectal cancers
    • Sjöblom T, et al. The consensus coding sequences of human breast and colorectal cancers. Sci 2006; 314: 268-274.
    • (2006) Sci , vol.314 , pp. 268-274
    • Sjöblom, T.1
  • 55
    • 15544377784 scopus 로고    scopus 로고
    • Database of mRNA gene expression profiles of multiple human organs
    • Son CG, et al. Database of mRNA gene expression profiles of multiple human organs. Genome Res. 2005; 15: 443-450.
    • (2005) Genome Res , vol.15 , pp. 443-450
    • Son, C.G.1
  • 56
    • 58149234398 scopus 로고    scopus 로고
    • Network reconstruction based on steady-state data
    • Sontag ED. Network reconstruction based on steady-state data. Essays Biochemistry 2008; 45: 161-176.
    • (2008) Essays Biochemistry , vol.45 , pp. 161-176
    • Sontag, E.D.1
  • 57
    • 0000658710 scopus 로고
    • Markov random fields and Gibbs ensembles
    • Spitzer F. Markov random fields and Gibbs ensembles. Am Math Month 1971; 78(2): 142-154.
    • (1971) Am Math Month , vol.78 , Issue.2 , pp. 142-154
    • Spitzer, F.1
  • 58
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Nat'l Acad Sci 2005; 102(43): 15545-15550.
    • (2005) Proc Nat'l Acad Sci , vol.102 , Issue.43 , pp. 15545-15550
    • Subramanian, A.1
  • 59
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • Tibshirani R et al. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Nat'l Acad Sci 2002; 99(10): 6567-6572.
    • (2002) Proc Nat'l Acad Sci , vol.99 , Issue.10 , pp. 6567-6572
    • Tibshirani, R.1
  • 60
    • 52949118488 scopus 로고    scopus 로고
    • Kras regulatory elements and exon 4A determine mutation specificity in lung cancer
    • To MD et al. Kras regulatory elements and exon 4A determine mutation specificity in lung cancer. Nat Genet 2008; 40(10): 1240-124.
    • (2008) Nat Genet , vol.40 , Issue.10 , pp. 1124-1240
    • To, M.D.1
  • 61
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation responses
    • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation responses. Proc Nat'l Acad Sci 2001; 98(9): 5116-5121.
    • (2001) Proc Nat'l Acad Sci , vol.98 , Issue.9 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 63
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Sci 2001; 291: 1304-1351.
    • (2001) Sci , vol.291 , pp. 1304-1351
    • Venter, J.C.1    Adams, M.D.2    Myers, E.W.3
  • 64
    • 70249108504 scopus 로고    scopus 로고
    • Genome-wide identification of post-translational modulators of transcription factor activity in human B cells
    • Wang K, et al. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol 2009; 27(9): 829-839.
    • (2009) Nat Biotechnol , vol.27 , Issue.9 , pp. 829-839
    • Wang, K.1
  • 65
    • 36248962105 scopus 로고    scopus 로고
    • The genomic landscapes of human breast and colorectal cancers
    • Wood LD, et al. The genomic landscapes of human breast and colorectal cancers. Sci 2007; 318: 1108-1113.
    • (2007) Sci , vol.318 , pp. 1108-1113
    • Wood, L.D.1
  • 66
    • 79956222046 scopus 로고    scopus 로고
    • Inferring stable genetic networks from steady-state data
    • Zavlanos MM, et al. Inferring stable genetic networks from steady-state data. Automatica 2011; 47(6): 1113-1122.
    • (2011) Automatica , vol.47 , Issue.6 , pp. 1113-1122
    • Zavlanos, M.M.1
  • 67
    • 43849084374 scopus 로고    scopus 로고
    • Inferring connectivity of genetic regulatory networks using information theoretic criteria
    • Zhao W, Serpedin E, Dougherty ER. Inferring connectivity of genetic regulatory networks using information theoretic criteria. IEEE/ACM Trans Comput Biol Bioinf 2008; 5(2): 262-274.
    • (2008) IEEE/ACM Trans Comput Biol Bioinf , vol.5 , Issue.2 , pp. 262-274
    • Zhao, W.1    Serpedin, E.2    Dougherty, E.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.