메뉴 건너뛰기




Volumn 10, Issue 3, 2006, Pages 276-288

Hidden markov model for defining genomic changes in lung cancer using gene expression data

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 33750935080     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2006.10.276     Document Type: Article
Times cited : (1)

References (34)
  • 1
    • 0034744639 scopus 로고    scopus 로고
    • Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer
    • BAYLIN, S.B., ESTELLER, M., ROUNTREE, M.R., et al. (2001). Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 10, 687-692.
    • (2001) Hum Mol Genet , vol.10 , pp. 687-692
    • Baylin, S.B.1    Esteller, M.2    Rountree, M.R.3
  • 2
    • 0000353178 scopus 로고
    • A maximization technique occurring in the statistical analysis of probabilistic functions of markov chains
    • BAUM, L.E., PETRIE, T., SOULES, G., et al. (1970). A maximization technique occurring in the statistical analysis of probabilistic functions of markov chains. Ann Math Stat 41, 164-171.
    • (1970) Ann Math Stat , vol.41 , pp. 164-171
    • Baum, L.E.1    Petrie, T.2    Soules, G.3
  • 3
    • 18544365698 scopus 로고    scopus 로고
    • Gene expression profiles predict survival of patients with lung adenocarcinoma
    • BEER, D.G., KARDIA, S.L.R., HUANG C.-C., et al. (2002). Gene expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8, 816-824.
    • (2002) Nat Med , vol.8 , pp. 816-824
    • Beer, D.G.1    Kardia, S.L.R.2    Huang, C.-C.3
  • 4
    • 13244268321 scopus 로고    scopus 로고
    • Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma
    • BISOGNIN, A., BORTOLUZZI, S., and DANIELI, G.A. (2004). Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma. BMC Bioinform 5, 68.
    • (2004) BMC Bioinform , vol.5 , pp. 68
    • Bisognin, A.1    Bortoluzzi, S.2    Danieli, G.A.3
  • 5
    • 0344734060 scopus 로고    scopus 로고
    • DNA gains in 3q occur frequently in squamous cell carcinoma of the lung, but not in adenocarcinoma
    • BJORKQVIST, A.M., HUSGAFVEL-PURSIAINEN, K., ANTTILA, S., et al. (1998). DNA gains in 3q occur frequently in squamous cell carcinoma of the lung, but not in adenocarcinoma. Genes Chromosomes Cancer 22, 79-82.
    • (1998) Genes Chromosomes Cancer , vol.22 , pp. 79-82
    • Bjorkqvist, A.M.1    Husgafvel-Pursiainen, K.2    Anttila, S.3
  • 6
    • 0035895502 scopus 로고    scopus 로고
    • The human transcriptome map: Clustering of highly expressed genes in chromosomal domain
    • CARON, H., VAN SCHAIK, B., VAN DER MEE, M., et al. (2001). The human transcriptome map: clustering of highly expressed genes in chromosomal domain. Science 291, 1289-1292.
    • (2001) Science , vol.291 , pp. 1289-1292
    • Caron, H.1    Van Schaik, B.2    Van Der Mee, M.3
  • 7
    • 0033780450 scopus 로고    scopus 로고
    • A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression
    • COHEN, B.A., MITRA, R.D., HUGHES, J.D., et al. (2000). A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26, 183-186.
    • (2000) Nat Genet , vol.26 , pp. 183-186
    • Cohen, B.A.1    Mitra, R.D.2    Hughes, J.D.3
  • 8
    • 0000336139 scopus 로고
    • Regression models and life tables
    • COX, D.R. (1972). Regression models and life tables J R Soc Stat B 34, 187-220.
    • (1972) J R Soc Stat B , vol.34 , pp. 187-220
    • Cox, D.R.1
  • 9
    • 3342915498 scopus 로고    scopus 로고
    • Integrated analysis of microarray data and gene function information
    • CUI, Y., ZHOU, M., and WONG, W.H. (2004). Integrated analysis of microarray data and gene function information. OMICS 8, 106-117.
    • (2004) OMICS , vol.8 , pp. 106-117
    • Cui, Y.1    Zhou, M.2    Wong, W.H.3
  • 11
    • 0037096897 scopus 로고    scopus 로고
    • A preliminary transcriptome map of non-small cell lung cancer
    • FUJII, T., DRACHEVA, T., PLAYER, A., et al. (2002). A preliminary transcriptome map of non-small cell lung cancer. Cancer Res 62, 3340-3346.
    • (2002) Cancer Res , vol.62 , pp. 3340-3346
    • Fujii, T.1    Dracheva, T.2    Player, A.3
  • 12
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    • GAO, P., FOAT, B.C., and BUSSEMAKER, H.J. (2004). Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinform 5, 31.
    • (2004) BMC Bioinform , vol.5 , pp. 31
    • Gao, P.1    Foat, B.C.2    Bussemaker, H.J.3
  • 13
    • 10844232112 scopus 로고    scopus 로고
    • Whole genome DNA copy number changes identified by high density oligonucleotide arrays
    • HUANG, J., WEI, W., ZHANG, J., et al. (2004). Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1, 287-299.
    • (2004) Hum Genomics , vol.1 , pp. 287-299
    • Huang, J.1    Wei, W.2    Zhang, J.3
  • 14
    • 0348143197 scopus 로고    scopus 로고
    • Combining DNA expression with positional information to detect functional silencing of chromosomal regions
    • HUSING, J., ZESCHNIGK, M., BOES, T., et al. (2003). Combining DNA expression with positional information to detect functional silencing of chromosomal regions. Bioinformatics 19, 2335-2342.
    • (2003) Bioinformatics , vol.19 , pp. 2335-2342
    • Husing, J.1    Zeschnigk, M.2    Boes, T.3
  • 16
    • 0031895154 scopus 로고    scopus 로고
    • DNA copy number amplification in human neoplasms: Review of comparative genomic hybridization studies
    • KNUUTILA S., BJORKQVIST, A.M., AUTIO, K., et al. (1998). DNA copy number amplification in human neoplasms: review of comparative genomic hybridization studies. Am J Pathol 152, 1107-1123.
    • (1998) Am J Pathol , vol.152 , pp. 1107-1123
    • Knuutila, S.1    Bjorkqvist, A.M.2    Autio, K.3
  • 17
    • 0032887168 scopus 로고    scopus 로고
    • DNA copy number losses in human neoplasms
    • KNUUTILA, S., AALTO, Y., AUTIO, K., et al. (1999). DNA copy number losses in human neoplasms. Am J Pathol 155, 683-694.
    • (1999) Am J Pathol , vol.155 , pp. 683-694
    • Knuutila, S.1    Aalto, Y.2    Autio, K.3
  • 18
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • LEE, T.I., RINALDI, H.J., ROBERT, F., et al. (2002). Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1    Rinaldi, H.J.2    Robert, F.3
  • 19
    • 0001572082 scopus 로고
    • Maximum-likelihood estimation for hidden Markov models
    • LEROUX, B.G. (1992). Maximum-likelihood estimation for hidden Markov models. Stochastic Proc Appl 40, 127-143.
    • (1992) Stochastic Proc Appl , vol.40 , pp. 127-143
    • Leroux, B.G.1
  • 20
    • 0026652789 scopus 로고
    • Maximum-penalized-likelihood estimation for independent and Markov-dependent mixture models
    • LEROUX, B.G., and PUTERMAN, M.L. (1992). Maximum-penalized-likelihood estimation for independent and Markov-dependent mixture models. Biometrics 48, 545-558.
    • (1992) Biometrics , vol.48 , pp. 545-558
    • Leroux, B.G.1    Puterman, M.L.2
  • 22
    • 20844454367 scopus 로고    scopus 로고
    • A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors
    • LEVIN, A.M., GHOSH, D., CHO, K.R., et al. (2005). A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors. Bioinformatics 21, 2867-2874.
    • (2005) Bioinformatics , vol.21 , pp. 2867-2874
    • Levin, A.M.1    Ghosh, D.2    Cho, K.R.3
  • 23
    • 2542548405 scopus 로고    scopus 로고
    • dChipSNP: Significance curve and clustering of SNP-array-based loss-of-heterozygosity data
    • LIN, M., WEI, L.J., SELLERS, W.R., et al. (2004). dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 20, 1233-1240.
    • (2004) Bioinformatics , vol.20 , pp. 1233-1240
    • Lin, M.1    Wei, L.J.2    Sellers, W.R.3
  • 25
    • 2442718023 scopus 로고    scopus 로고
    • Using protein-protein interactions for re-fining gene networls estimated from microarray data by Bayesian networks
    • NARIAI, N., KIM, S., IMOTO, S., et al. (2004). Using protein-protein interactions for re-fining gene networls estimated from microarray data by Bayesian networks. Proc Pac Symp Biocomput 9, 336-347.
    • (2004) Proc Pac Symp Biocomput , vol.9 , pp. 336-347
    • Nariai, N.1    Kim, S.2    Imoto, S.3
  • 26
    • 0032823523 scopus 로고    scopus 로고
    • Genome-wide analysis of DNA copy-number changes using cDNA microarrays
    • POLLACK, J.R., PEROU, C.M., ALIZADEH, A.A., et al. (1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23, 41-46.
    • (1999) Nat Genet , vol.23 , pp. 41-46
    • Pollack, J.R.1    Perou, C.M.2    Alizadeh, A.A.3
  • 27
    • 13844250828 scopus 로고    scopus 로고
    • Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
    • POLLACK, J.R., SRLIE, T., PEROU, C.M., et al. (2002). Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 99, 12963-12968.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12963-12968
    • Pollack, J.R.1    Srlie, T.2    Perou, C.M.3
  • 28
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • RABINER, L.R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77, 257-286.
    • (1989) Proc IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 29
    • 0021404166 scopus 로고
    • Mixture densities, maximum likelihood and the EM algorithm
    • REDNER, R.A. and WALKER, H.F. (1984). Mixture densities, maximum likelihood and the EM algorithm. Soc Indust Appl Math Rev 26, 195-239.
    • (1984) Soc Indust Appl Math Rev , vol.26 , pp. 195-239
    • Redner, R.A.1    Walker, H.F.2
  • 30
    • 0003897447 scopus 로고
    • Academic Press, San Diego
    • th ed. (Academic Press, San Diego).
    • (1993) th Ed.
    • Ross, S.M.1
  • 31
    • 0003328368 scopus 로고    scopus 로고
    • Evidence for large domains of similarly expressed genes in the Drosophila genome
    • SPELLMAN, P.T., and RUBIN, G.M. (2002). Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1, 5.
    • (2002) J Biol , vol.1 , pp. 5
    • Spellman, P.T.1    Rubin, G.M.2
  • 32
    • 3242891560 scopus 로고    scopus 로고
    • Estimating gene networks from gene expression data by combining Bayesian netowrk model with promoter element detection
    • TAMADA, Y., KIM, S., BANNAI, H., et al. (2003). Estimating gene networks from gene expression data by combining Bayesian netowrk model with promoter element detection. Bioinformatics Suppl. 2, 227-236.
    • (2003) Bioinformatics , Issue.SUPPL. 2 , pp. 227-236
    • Tamada, Y.1    Kim, S.2    Bannai, H.3
  • 33
    • 4043181214 scopus 로고    scopus 로고
    • Cancer genes and the pathways they control
    • VOGELSTEIN, B., and KINZLER, K.W. (2004). Cancer genes and the pathways they control. Nat Med 10, 789-799.
    • (2004) Nat Med , vol.10 , pp. 789-799
    • Vogelstein, B.1    Kinzler, K.W.2
  • 34
    • 0036790999 scopus 로고    scopus 로고
    • Transitive functional annotation by shortest path analysis of gene expression data
    • ZHOU, X., KAO, M.J., and WONG, W.H. (2002). Transitive functional annotation by shortest path analysis of gene expression data. Proc Natl Acad Sci USA 99, 12783-12788.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12783-12788
    • Zhou, X.1    Kao, M.J.2    Wong, W.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.