메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

A semi-parametric Bayesian model for unsupervised differential co-expression analysis

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SAMPLES; EXPRESSION PATTERNS; GENE EXPRESSION LEVELS; GENE EXPRESSION PROFILES; PROBABILISTIC FRAMEWORK; REGULATORY NETWORK; SIMILARITY MEASURE; UNSUPERVISED ANALYSIS;

EID: 77951944123     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-234     Document Type: Article
Times cited : (34)

References (56)
  • 1
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus
    • 10.1038/nrg1749, 16369572
    • Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 2006, 7:55-65. 10.1038/nrg1749, 16369572.
    • (2006) Nat Rev Genet , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 2
    • 33846606051 scopus 로고    scopus 로고
    • Clustering methods for microarray gene expression data
    • 10.1089/omi.2006.10.507, 17233561
    • Belacel N, Wang Q, Cuperlovic-Culf M. Clustering methods for microarray gene expression data. OMICS 2006, 10:507-531. 10.1089/omi.2006.10.507, 17233561.
    • (2006) OMICS , vol.10 , pp. 507-531
    • Belacel, N.1    Wang, Q.2    Cuperlovic-Culf, M.3
  • 3
    • 39449097889 scopus 로고    scopus 로고
    • Techniques for clustering gene expression data
    • 10.1016/j.compbiomed.2007.11.001, 18061589
    • Kerr G, Ruskin HJ, Crane M, Doolan P. Techniques for clustering gene expression data. Comput Biol Med 2008, 38:283-293. 10.1016/j.compbiomed.2007.11.001, 18061589.
    • (2008) Comput Biol Med , vol.38 , pp. 283-293
    • Kerr, G.1    Ruskin, H.J.2    Crane, M.3    Doolan, P.4
  • 4
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    • 10.1073/pnas.96.12.6745, 21986, 10359783
    • Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 1999, 96:6745-6750. 10.1073/pnas.96.12.6745, 21986, 10359783.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 6745-6750
    • Alon, U.1    Barkai, N.2    Notterman, D.A.3    Gish, K.4    Ybarra, S.5    Mack, D.6    Levine, A.J.7
  • 6
    • 11244306358 scopus 로고    scopus 로고
    • Discovering statistically significant biclusters in gene expression data
    • Tanay A, Sharan R, Shamir R. Discovering statistically significant biclusters in gene expression data. Bioinformatics 2002, 18(Suppl 1):S136-S144.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Tanay, A.1    Sharan, R.2    Shamir, R.3
  • 7
    • 33845864692 scopus 로고    scopus 로고
    • Computing the maximum similarity bi-clusters of gene expression data
    • 10.1093/bioinformatics/btl560, 17090578
    • Liu X, Wang L. Computing the maximum similarity bi-clusters of gene expression data. Bioinformatics 2007, 23:50-56. 10.1093/bioinformatics/btl560, 17090578.
    • (2007) Bioinformatics , vol.23 , pp. 50-56
    • Liu, X.1    Wang, L.2
  • 10
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • 10.1038/ng1165, 12740579
    • Segal E, Shpira M, Regev A, Pe'er D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:166-176. 10.1038/ng1165, 12740579.
    • (2003) Nat Genet , vol.34 , pp. 166-176
    • Segal, E.1    Shpira, M.2    Regev, A.3    Pe'er, D.4    Koller, D.5    Friedman, N.6
  • 11
    • 33746067911 scopus 로고    scopus 로고
    • Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
    • 10.1186/1471-2105-7-280, 1502140, 16749936
    • Reiss DJ, Baliga NS, Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 2006, 7:280. 10.1186/1471-2105-7-280, 1502140, 16749936.
    • (2006) BMC Bioinformatics , vol.7 , pp. 280
    • Reiss, D.J.1    Baliga, N.S.2    Bonneau, R.3
  • 13
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • 10.1093/bioinformatics/bti722, 16234317
    • Choi JK, Yu U, Yoo OJ, Kim S. Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 2005, 21:4348-4355. 10.1093/bioinformatics/bti722, 16234317.
    • (2005) Bioinformatics , vol.21 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 14
    • 65549155929 scopus 로고    scopus 로고
    • Identifying set-wise differential co-expression in gene expression microarray data
    • 10.1186/1471-2105-10-109, 2679020, 19371436
    • Cho SB, Kim J, Kim JH. Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics 2009, 10:109. 10.1186/1471-2105-10-109, 2679020, 19371436.
    • (2009) BMC Bioinformatics , vol.10 , pp. 109
    • Cho, S.B.1    Kim, J.2    Kim, J.H.3
  • 15
    • 70350682038 scopus 로고    scopus 로고
    • Statistical Methods for Gene Set Co-expression Analysis
    • Choi Y, Kendziorski C. Statistical Methods for Gene Set Co-expression Analysis. Bioinformatics 2009,
    • (2009) Bioinformatics
    • Choi, Y.1    Kendziorski, C.2
  • 16
    • 10244219943 scopus 로고    scopus 로고
    • A statistical method for identifying differential gene-gene co-expression patterns
    • 10.1093/bioinformatics/bth379, 15231528
    • Lai Y, Wu B, Chen L, Zhao H. A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics 2004, 20:3146-3155. 10.1093/bioinformatics/bth379, 15231528.
    • (2004) Bioinformatics , vol.20 , pp. 3146-3155
    • Lai, Y.1    Wu, B.2    Chen, L.3    Zhao, H.4
  • 17
    • 21044446187 scopus 로고    scopus 로고
    • Finding disease specific alterations in the co-expression of genes
    • 10.1093/bioinformatics/bth909, 15262799
    • Kostka D, Spang R. Finding disease specific alterations in the co-expression of genes. Bioinformatics 2004, 20(Suppl 1):i194-i199. 10.1093/bioinformatics/bth909, 15262799.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Kostka, D.1    Spang, R.2
  • 18
    • 34547649056 scopus 로고    scopus 로고
    • CoXpress: differential co-expression in gene expression data
    • 10.1186/1471-2105-7-509, 1660556, 17116249
    • Watson M. CoXpress: differential co-expression in gene expression data. BMC Bioinformatics 2006, 7:509. 10.1186/1471-2105-7-509, 1660556, 17116249.
    • (2006) BMC Bioinformatics , vol.7 , pp. 509
    • Watson, M.1
  • 19
    • 67049159812 scopus 로고    scopus 로고
    • A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    • 10.1371/journal.pcbi.1000382, 2671163, 19412532
    • Hudson NJ, Reverter A, Dalrymple BP. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 2009, 5:e1000382. 10.1371/journal.pcbi.1000382, 2671163, 19412532.
    • (2009) PLoS Comput Biol , vol.5
    • Hudson, N.J.1    Reverter, A.2    Dalrymple, B.P.3
  • 20
    • 0001120413 scopus 로고
    • A Bayesian analysis of some nonparametric problems
    • Ferguson TS. A Bayesian analysis of some nonparametric problems. The Annals of Statistics 1973, 1:209-230.
    • (1973) The Annals of Statistics , vol.1 , pp. 209-230
    • Ferguson, T.S.1
  • 21
    • 77950032550 scopus 로고    scopus 로고
    • Markov Chain Sampling Methods for Dirichlet Process Mixture Models
    • Neal RM. Markov Chain Sampling Methods for Dirichlet Process Mixture Models. Journal of Computational and Graphical Statistics 2000, 9:249-265.
    • (2000) Journal of Computational and Graphical Statistics , vol.9 , pp. 249-265
    • Neal, R.M.1
  • 22
    • 77953682731 scopus 로고    scopus 로고
    • Identifying statistically significant patterns of expression via Bayesian Infinite Mixture Models
    • Medvedovic M. Identifying statistically significant patterns of expression via Bayesian Infinite Mixture Models. Critical Assessment of Microarray Data Analysis (CAMDA) 2000,
    • (2000) Critical Assessment of Microarray Data Analysis (CAMDA)
    • Medvedovic, M.1
  • 23
    • 0036739286 scopus 로고    scopus 로고
    • Bayesian infinite mixture model based clustering of gene expression profiles
    • 10.1093/bioinformatics/18.9.1194, 12217911
    • Medvedovic M, Sivaganesan S. Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics 2002, 18:1194-1206. 10.1093/bioinformatics/18.9.1194, 12217911.
    • (2002) Bioinformatics , vol.18 , pp. 1194-1206
    • Medvedovic, M.1    Sivaganesan, S.2
  • 24
    • 3042686005 scopus 로고    scopus 로고
    • Bayesian mixture model based clustering of replicated microarray data
    • 10.1093/bioinformatics/bth068, 14871871
    • Medvedovic M, Yeung KY, Bumgarner RE. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics 2004, 20:1222-1232. 10.1093/bioinformatics/bth068, 14871871.
    • (2004) Bioinformatics , vol.20 , pp. 1222-1232
    • Medvedovic, M.1    Yeung, K.Y.2    Bumgarner, R.E.3
  • 25
    • 33749402477 scopus 로고    scopus 로고
    • Bayesian Model-Averaging in Unsupervised Learing From Microarray Data
    • Medvedovic M, Guo J. Bayesian Model-Averaging in Unsupervised Learing From Microarray Data. BIOKDD 2004,
    • (2004) BIOKDD
    • Medvedovic, M.1    Guo, J.2
  • 26
    • 33747875436 scopus 로고    scopus 로고
    • Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
    • 10.1093/bioinformatics/btl184, 1617036, 16709591
    • Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics 2006, 22:1737-1744. 10.1093/bioinformatics/btl184, 1617036, 16709591.
    • (2006) Bioinformatics , vol.22 , pp. 1737-1744
    • Liu, X.1    Sivaganesan, S.2    Yeung, K.Y.3    Guo, J.4    Bumgarner, R.E.5    Medvedovic, M.6
  • 27
    • 34848855728 scopus 로고    scopus 로고
    • Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
    • 10.1186/1471-2105-8-283, 1994961, 17683565
    • Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M. Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC Bioinformatics 2007, 8:283. 10.1186/1471-2105-8-283, 1994961, 17683565.
    • (2007) BMC Bioinformatics , vol.8 , pp. 283
    • Liu, X.1    Jessen, W.J.2    Sivaganesan, S.3    Aronow, B.J.4    Medvedovic, M.5
  • 32
    • 60849097255 scopus 로고    scopus 로고
    • Gene-expression signatures in breast cancer
    • 10.1056/NEJMra0801289, 19228622
    • Sotiriou C, Pusztai L. Gene-expression signatures in breast cancer. N Engl J Med 2009, 360:790-800. 10.1056/NEJMra0801289, 19228622.
    • (2009) N Engl J Med , vol.360 , pp. 790-800
    • Sotiriou, C.1    Pusztai, L.2
  • 36
    • 33646894725 scopus 로고    scopus 로고
    • BicAT: a biclustering analysis toolbox
    • 10.1093/bioinformatics/btl099, 16551664
    • Barkow S, Bleuler S, Prelic A, Zimmermann P, Zitzler E. BicAT: a biclustering analysis toolbox. Bioinformatics 2006, 22:1282-1283. 10.1093/bioinformatics/btl099, 16551664.
    • (2006) Bioinformatics , vol.22 , pp. 1282-1283
    • Barkow, S.1    Bleuler, S.2    Prelic, A.3    Zimmermann, P.4    Zitzler, E.5
  • 39
    • 52949124120 scopus 로고    scopus 로고
    • A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
    • 10.1093/bioinformatics/btn374, 2553442, 18635567
    • Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?. Bioinformatics 2008, 24:2200-2208. 10.1093/bioinformatics/btn374, 2553442, 18635567.
    • (2008) Bioinformatics , vol.24 , pp. 2200-2208
    • Haibe-Kains, B.1    Desmedt, C.2    Sotiriou, C.3    Bontempi, G.4
  • 40
    • 26444546442 scopus 로고    scopus 로고
    • From The Cover: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    • 10.1073/pnas.0506230102, 1197273, 16141321
    • Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, et al. From The Cover: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. PNAS 2005, 102:13550-13555. 10.1073/pnas.0506230102, 1197273, 16141321.
    • (2005) PNAS , vol.102 , pp. 13550-13555
    • Miller, L.D.1    Smeds, J.2    George, J.3    Vega, V.B.4    Vergara, L.5    Ploner, A.6    Pawitan, Y.7    Hall, P.8    Klaar, S.9    Liu, E.T.10
  • 41
    • 34250652449 scopus 로고    scopus 로고
    • Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series
    • 10.1158/1078-0432.CCR-06-2765, 17545524
    • Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, et al. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res 2007, 13:3207-3214. 10.1158/1078-0432.CCR-06-2765, 17545524.
    • (2007) Clin Cancer Res , vol.13 , pp. 3207-3214
    • Desmedt, C.1    Piette, F.2    Loi, S.3    Wang, Y.4    Lallemand, F.5    Haibe-Kains, B.6    Viale, G.7    Delorenzi, M.8    Zhang, Y.9    d'Assignies, M.S.10
  • 42
    • 34447632167 scopus 로고    scopus 로고
    • Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts
    • 10.1186/bcr1325, 1410752, 16280042
    • Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 2005, 7:R953-R964. 10.1186/bcr1325, 1410752, 16280042.
    • (2005) Breast Cancer Res , vol.7
    • Pawitan, Y.1    Bjohle, J.2    Amler, L.3    Borg, A.L.4    Egyhazi, S.5    Hall, P.6    Han, X.7    Holmberg, L.8    Huang, F.9    Klaar, S.10
  • 43
    • 44949121510 scopus 로고    scopus 로고
    • Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen
    • 10.1186/1471-2164-9-239, 2423197, 18498629
    • Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 2008, 9:239. 10.1186/1471-2164-9-239, 2423197, 18498629.
    • (2008) BMC Genomics , vol.9 , pp. 239
    • Loi, S.1    Haibe-Kains, B.2    Desmedt, C.3    Wirapati, P.4    Lallemand, F.5    Tutt, A.M.6    Gillet, C.7    Ellis, P.8    Ryder, K.9    Reid, J.F.10
  • 44
    • 38349095526 scopus 로고    scopus 로고
    • Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells
    • 10.1093/nar/gkm945, 2248750, 17986456
    • Bourdeau V, Deschenes J, Laperriere D, Aid M, White JH, Mader S. Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. Nucl Acids Res 2008, 36:76-93. 10.1093/nar/gkm945, 2248750, 17986456.
    • (2008) Nucl Acids Res , vol.36 , pp. 76-93
    • Bourdeau, V.1    Deschenes, J.2    Laperriere, D.3    Aid, M.4    White, J.H.5    Mader, S.6
  • 45
    • 17844386351 scopus 로고    scopus 로고
    • Anti-proliferative effect of estrogen in breast cancer cells that re-express ER{alpha} is mediated by aberrant regulation of cell cycle genes
    • 10.1677/jme.1.01677, 15821115
    • Moggs JG, Murphy TC, Lim FL, Moore DJ, Stuckey R, Antrobus K, Kimber I, Orphanides G. Anti-proliferative effect of estrogen in breast cancer cells that re-express ER{alpha} is mediated by aberrant regulation of cell cycle genes. J Mol Endocrinol 2005, 34:535-551. 10.1677/jme.1.01677, 15821115.
    • (2005) J Mol Endocrinol , vol.34 , pp. 535-551
    • Moggs, J.G.1    Murphy, T.C.2    Lim, F.L.3    Moore, D.J.4    Stuckey, R.5    Antrobus, K.6    Kimber, I.7    Orphanides, G.8
  • 47
    • 72549085551 scopus 로고    scopus 로고
    • Genomic actions of estrogen receptor {alpha}: what are the targets and how are they regulated?
    • ERC-09
    • Welboren WJ, Sweep FCGJ, Span P, Stunnenberg H. Genomic actions of estrogen receptor {alpha}: what are the targets and how are they regulated?. Endocr Relat Cancer 2009, ERC-09.
    • (2009) Endocr Relat Cancer
    • Welboren, W.J.1    Sweep, F.C.G.J.2    Span, P.3    Stunnenberg, H.4
  • 48
    • 58249103214 scopus 로고    scopus 로고
    • Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists
    • 10.1186/1755-8794-1-11, 2396170, 18439262
    • Mosley JD, Keri RA. Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists. BMC Med Genomics 2008, 1:11. 10.1186/1755-8794-1-11, 2396170, 18439262.
    • (2008) BMC Med Genomics , vol.1 , pp. 11
    • Mosley, J.D.1    Keri, R.A.2
  • 52
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 55
    • 69549095896 scopus 로고    scopus 로고
    • CLEAN: CLustering Enrichment ANalysis
    • 10.1186/1471-2105-10-234, 2734555, 19640299
    • Freudenberg JM, Joshi VK, Hu Z, Medvedovic M. CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics 2009, 10:234. 10.1186/1471-2105-10-234, 2734555, 19640299.
    • (2009) BMC Bioinformatics , vol.10 , pp. 234
    • Freudenberg, J.M.1    Joshi, V.K.2    Hu, Z.3    Medvedovic, M.4
  • 56
    • 58349105009 scopus 로고    scopus 로고
    • LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data
    • 10.1093/bioinformatics/btn592, 2639007, 19038984
    • Sartor MA, Leikauf GD, Medvedovic M. LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics 2009, 25:211-217. 10.1093/bioinformatics/btn592, 2639007, 19038984.
    • (2009) Bioinformatics , vol.25 , pp. 211-217
    • Sartor, M.A.1    Leikauf, G.D.2    Medvedovic, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.