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Volumn 68, Issue 2, 2012, Pages 455-465

An Empirical Bayesian Approach for Identifying Differential Coexpression in High-Throughput Experiments

Author keywords

Coexpression; Differential expression; Empirical bayes; Gene expression; Meta analysis; Microarray

Indexed keywords

BAYESIAN NETWORKS; IMAGE SEGMENTATION; MAXIMUM PRINCIPLE; THROUGHPUT;

EID: 84862889045     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2011.01688.x     Document Type: Article
Times cited : (40)

References (42)
  • 1
    • 60149104156 scopus 로고    scopus 로고
    • A statistical framework for testing functional categories in microarray data
    • Barry, W. T., Nobel, A. B., and Wright, F. A. (2008). A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2, 286-315.
    • (2008) Annals of Applied Statistics , vol.2 , pp. 286-315
    • Barry, W.T.1    Nobel, A.B.2    Wright, F.A.3
  • 2
    • 0001028358 scopus 로고
    • An inverse matrix adjustment arising in discriminant analysis
    • Bartlett, M. S. (1951). An inverse matrix adjustment arising in discriminant analysis. Annals of Mathematical Statistics 22, 107-111.
    • (1951) Annals of Mathematical Statistics , vol.22 , pp. 107-111
    • Bartlett, M.S.1
  • 3
    • 32644460955 scopus 로고
    • Linear modelling of Pearson's product moment correlation coefficient: an application of Fisher's z-transformation
    • Bartlett, R. F. (1993). Linear modelling of Pearson's product moment correlation coefficient: an application of Fisher's z-transformation. Journal of the Royal Statistical Society, Series D 42, 45-53.
    • (1993) Journal of the Royal Statistical Society, Series D , vol.42 , pp. 45-53
    • Bartlett, R.F.1
  • 6
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on bias and variance
    • Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 7
    • 0036401627 scopus 로고    scopus 로고
    • Bayesian hierarchical model for identifying changes in gene expression from microarray experiments
    • Broet, P., Richardson, S., and Radvanyi, F. (2002). Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. Journal of Computational Biology 9, 671-683.
    • (2002) Journal of Computational Biology , vol.9 , pp. 671-683
    • Broet, P.1    Richardson, S.2    Radvanyi, F.3
  • 9
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • Choi, J. K., Yu, U., Yoo, O. J., and Kim, S. (2005). Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21, 4348-4355.
    • (2005) Bioinformatics , vol.21 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 10
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking'-identification of dysfunctional regulatory networks in diseases
    • de la Fuente, A. (2010). From 'differential expression' to 'differential networking'-identification of dysfunctional regulatory networks in diseases. Trends in Genetics 26, 326-333.
    • (2010) Trends in Genetics , vol.26 , pp. 326-333
    • de la Fuente, A.1
  • 12
    • 0001727379 scopus 로고
    • The general sampling distribution of the multiple correlation coefficient
    • Fisher, R. A. (1928). The general sampling distribution of the multiple correlation coefficient. Journal of the Royal Statistical Society, Series A 121, 654-673.
    • (1928) Journal of the Royal Statistical Society, Series A , vol.121 , pp. 654-673
    • Fisher, R.A.1
  • 14
    • 85153156049 scopus 로고    scopus 로고
    • MCLUST version 3 for R: Normal mixture modeling and model-based clustering (revised 2009). Technical Report 504, Department of Statistics, University of Washington, Seattle, WA.
    • Fraley, C. and Raftery, A. E. (2006). MCLUST version 3 for R: Normal mixture modeling and model-based clustering (revised 2009). Technical Report 504, Department of Statistics, University of Washington, Seattle, WA
    • (2006)
    • Fraley, C.1    Raftery, A.E.2
  • 17
    • 62749083987 scopus 로고    scopus 로고
    • Detecting intergene correlation changes in microarray analysis: A new approach to gene selection
    • Hu, R., Qiu, X., Glazko, G., Klebanov, L., and Yakovlev, A. (2009). Detecting intergene correlation changes in microarray analysis: A new approach to gene selection. BMC Bioinformatics 10, 20.
    • (2009) BMC Bioinformatics , vol.10 , pp. 20
    • Hu, R.1    Qiu, X.2    Glazko, G.3    Klebanov, L.4    Yakovlev, A.5
  • 18
    • 77949517089 scopus 로고    scopus 로고
    • A new gene selection procedure based on the covariance distance
    • Hu, R., Qiu, X., and Glazko, G. (2010). A new gene selection procedure based on the covariance distance. Bioinformatics 26, 348-354.
    • (2010) Bioinformatics , vol.26 , pp. 348-354
    • Hu, R.1    Qiu, X.2    Glazko, G.3
  • 20
    • 0141792846 scopus 로고    scopus 로고
    • Expression of replication-licensing factors MCM2 and MCM3 in normal, hyperplastic, and carcinomatous endometrium: Correlation with expression of Ki-67 and estrogen and progesterone receptors
    • Kato, K., Toki, T., Shimizu, M., Shiozawa, T., Fujii, S., Nakaido, T., and Konishi, I. (2003). Expression of replication-licensing factors MCM2 and MCM3 in normal, hyperplastic, and carcinomatous endometrium: Correlation with expression of Ki-67 and estrogen and progesterone receptors. Internation Journal of Gynecological Pathology 22, 334-340.
    • (2003) Internation Journal of Gynecological Pathology , vol.22 , pp. 334-340
    • Kato, K.1    Toki, T.2    Shimizu, M.3    Shiozawa, T.4    Fujii, S.5    Nakaido, T.6    Konishi, I.7
  • 22
    • 0346888587 scopus 로고    scopus 로고
    • On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
    • Kendziorski, C. M., Newton, M. A., Lan, H., and Gould, M. N. (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistics in Medicine 22, 3899-3914.
    • (2003) Statistics in Medicine , vol.22 , pp. 3899-3914
    • Kendziorski, C.M.1    Newton, M.A.2    Lan, H.3    Gould, M.N.4
  • 23
    • 10244219943 scopus 로고    scopus 로고
    • A statistical method for identifying differential gene-gene co-expression patterns
    • Lai, Y., Wu, B., Chen, L., and Zhao, H. (2004). A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics 20, 3146-3155.
    • (2004) Bioinformatics , vol.20 , pp. 3146-3155
    • Lai, Y.1    Wu, B.2    Chen, L.3    Zhao, H.4
  • 24
    • 0035629944 scopus 로고    scopus 로고
    • Is the property of being positively correlated transitive?
    • Langford, E., Schwertman, N., and Owens, M. (2001). Is the property of being positively correlated transitive? The American Statistician 55, 322-325.
    • (2001) The American Statistician , vol.55 , pp. 322-325
    • Langford, E.1    Schwertman, N.2    Owens, M.3
  • 25
    • 0037168518 scopus 로고    scopus 로고
    • Genome-wide coexpression dynamics: Theory and application
    • Li, K.-C. (2002). Genome-wide coexpression dynamics: Theory and application. PNAS 99, 16875-16880.
    • (2002) PNAS , vol.99 , pp. 16875-16880
    • Li, K.-C.1
  • 28
    • 74049143935 scopus 로고    scopus 로고
    • Dissecting the dynamics of dysregulation of cellular processes in mouse mammary glad tumor
    • Mentzen, W. I., Floris, M., and de la Fuente, A. (2009). Dissecting the dynamics of dysregulation of cellular processes in mouse mammary glad tumor. BMC Genomics 10, 601.
    • (2009) BMC Genomics , vol.10 , pp. 601
    • Mentzen, W.I.1    Floris, M.2    de la Fuente, A.3
  • 30
    • 34548329530 scopus 로고    scopus 로고
    • A perspective on dna microarrays in pathology research and practice
    • Pollack, J. R. (2007). A perspective on dna microarrays in pathology research and practice. American Journal of Pathology 171, 375-385.
    • (2007) American Journal of Pathology , vol.171 , pp. 375-385
    • Pollack, J.R.1
  • 32
    • 25444485444 scopus 로고    scopus 로고
    • The effects of normalization on the correlation structure of microarray data
    • Qiu, X., Brooks, A. I., Klebanov, L., and Yakovlev, A. (2005). The effects of normalization on the correlation structure of microarray data. BMC Bioinformatics 6, 120.
    • (2005) BMC Bioinformatics , vol.6 , pp. 120
    • Qiu, X.1    Brooks, A.I.2    Klebanov, L.3    Yakovlev, A.4
  • 33
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team. Vienna, Austria : R Foundation for Statistical Computing. Available at: Accessed August 11, 2011.
    • R Development Core Team. (2009). R: A Language and Environment for Statistical Computing. Vienna, Austria : R Foundation for Statistical Computing. Available at: Accessed August 11, 2011.
    • (2009) R: A Language and Environment for Statistical Computing
  • 34
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber (eds), New York : Springer.
    • Smyth, G. K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber (eds), 397-420. New York : Springer.
    • (2005) Bioinformatics and Computational Biology Solutions using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 37
    • 0031880105 scopus 로고    scopus 로고
    • Isolation of a novel tp53 target gene from a colon cancer cell line carrying a highly regulated wild-type tp53
    • Takei, Y., Ishikawa, S., Tokino, T., Muto, T., and Nakamura, Y. (1998). Isolation of a novel tp53 target gene from a colon cancer cell line carrying a highly regulated wild-type tp53. Genes, Chromosomes and Cancer 23, 1-9.
    • (1998) Genes, Chromosomes and Cancer , vol.23 , pp. 1-9
    • Takei, Y.1    Ishikawa, S.2    Tokino, T.3    Muto, T.4    Nakamura, Y.5
  • 38
    • 85153153034 scopus 로고    scopus 로고
    • The Human Gene Compendium. prostate androgen-regulated mucin-like protein 1. Available at: Accessed August 11, 2011.
    • The Human Gene Compendium. (2011). prostate androgen-regulated mucin-like protein 1. Available at: Accessed August 11, 2011.
    • (2011)
  • 39
    • 34547649056 scopus 로고    scopus 로고
    • Coxpress: Differential co-expression in gene expression data
    • Watson, M. (2006). Coxpress: Differential co-expression in gene expression data. BMC Bioinformatics 7, 509.
    • (2006) BMC Bioinformatics , vol.7 , pp. 509
    • Watson, M.1
  • 42
    • 35748952199 scopus 로고    scopus 로고
    • A gene expression bar code for microarray data
    • Zilliox, M. J. and Irizarry, R. A. (2007). A gene expression bar code for microarray data. Nature Methods 4, 911-913.
    • (2007) Nature Methods , vol.4 , pp. 911-913
    • Zilliox, M.J.1    Irizarry, R.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.