메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL STUDIES; CONFIDENCE INTERVAL; DIFFERENTIAL EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; GAUSSIAN PROCESS REGRESSION; GAUSSIAN PROCESSES; GENE EXPRESSION TIME SERIES; HIERARCHICAL BAYESIAN MODELING;

EID: 79956211692     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-180     Document Type: Article
Times cited : (77)

References (34)
  • 3
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • 10.1089/106652700750050961, 11108481
    • Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. Journal of computational biology 2000, 7(3-4):601-620. 10.1089/106652700750050961, 11108481.
    • (2000) Journal of computational biology , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'er, D.4
  • 4
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica sinica 2002, 12:111-140.
    • (2002) Statistica sinica , vol.12 , pp. 111-140
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 5
    • 0034927555 scopus 로고    scopus 로고
    • Analysis of variance for gene expression microarray data
    • 10.1089/10665270050514954, 11382364
    • Kerr MK, Martin M, Churchill GA. Analysis of variance for gene expression microarray data. Journal of Computational Biology 2000, 7(6):819-837. 10.1089/10665270050514954, 11382364.
    • (2000) Journal of Computational Biology , vol.7 , Issue.6 , pp. 819-837
    • Kerr, M.K.1    Martin, M.2    Churchill, G.A.3
  • 8
    • 28644452470 scopus 로고    scopus 로고
    • Clustering short time series gene expression data
    • 10.1093/bioinformatics/bti1022, 15961453
    • Ernst J, Nau G, Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics 2005, 21(Suppl 1):i159. 10.1093/bioinformatics/bti1022, 15961453.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Ernst, J.1    Nau, G.2    Bar-Joseph, Z.3
  • 10
    • 33750414249 scopus 로고    scopus 로고
    • A multivariate empirical Bayes statistic for replicated microarray time course data
    • Tai YC, Speed TP. A multivariate empirical Bayes statistic for replicated microarray time course data. The Annals of Statistics 2006, 34(5):2387-2412.
    • (2006) The Annals of Statistics , vol.34 , Issue.5 , pp. 2387-2412
    • Tai, Y.C.1    Speed, T.P.2
  • 12
    • 55449128330 scopus 로고    scopus 로고
    • BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
    • 10.1186/1471-2105-9-415, 2579305, 18837969
    • Angelini C, Cutillo L, De Canditiis D, Mutarelli M, Pensky M. BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments. BMC bioinformatics 2008, 9:415. 10.1186/1471-2105-9-415, 2579305, 18837969.
    • (2008) BMC bioinformatics , vol.9 , pp. 415
    • Angelini, C.1    Cutillo, L.2    De Canditiis, D.3    Mutarelli, M.4    Pensky, M.5
  • 13
    • 44849118743 scopus 로고    scopus 로고
    • Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
    • 10.1101/gr.073601.107, 2413161, 18441228
    • Della Gatta G, Bansal M, Ambesi-Impiombato A, Antonini D, Missero C, di Bernardo D. Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Genome research 2008, 18(6):939. 10.1101/gr.073601.107, 2413161, 18441228.
    • (2008) Genome research , vol.18 , Issue.6 , pp. 939
    • Della Gatta, G.1    Bansal, M.2    Ambesi-Impiombato, A.3    Antonini, D.4    Missero, C.5    di Bernardo, D.6
  • 15
    • 33645307955 scopus 로고    scopus 로고
    • Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
    • 10.1093/bioinformatics/btl003, 16418235
    • Bansal M, Gatta GD, Di Bernardo D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 2006, 22(7):815. 10.1093/bioinformatics/btl003, 16418235.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 815
    • Bansal, M.1    Gatta, G.D.2    Di Bernardo, D.3
  • 17
    • 8844277626 scopus 로고    scopus 로고
    • Analyzing time series gene expression data
    • 10.1093/bioinformatics/bth283, 15130923
    • Bar-Joseph Z. Analyzing time series gene expression data. Bioinformatics 2004, 20(16):2493. 10.1093/bioinformatics/bth283, 15130923.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2493
    • Bar-Joseph, Z.1
  • 18
    • 8444245968 scopus 로고    scopus 로고
    • Temporal aggregation bias and inference of causal regulatory networks
    • 10.1089/cmb.2004.11.971, 15700412
    • Bay SD, Chrisman L, Pohorille A, Shrager J. Temporal aggregation bias and inference of causal regulatory networks. Journal of Computational Biology 2004, 11(5):971-985. 10.1089/cmb.2004.11.971, 15700412.
    • (2004) Journal of Computational Biology , vol.11 , Issue.5 , pp. 971-985
    • Bay, S.D.1    Chrisman, L.2    Pohorille, A.3    Shrager, J.4
  • 19
    • 77950803115 scopus 로고    scopus 로고
    • A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series
    • 10.1089/cmb.2009.0175, 20377450
    • Stegle O, Denby KJ, Cooke EJ, Wild DL, Ghahramani Z, Borgwardt KM. A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. Journal of Computational Biology 2010, 17(3):355-367. 10.1089/cmb.2009.0175, 20377450.
    • (2010) Journal of Computational Biology , vol.17 , Issue.3 , pp. 355-367
    • Stegle, O.1    Denby, K.J.2    Cooke, E.J.3    Wild, D.L.4    Ghahramani, Z.5    Borgwardt, K.M.6
  • 20
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 10.1126/science.270.5235.467, 7569999
    • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467. 10.1126/science.270.5235.467, 7569999.
    • (1995) Science , vol.270 , Issue.5235 , pp. 467
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 23
    • 33750683623 scopus 로고    scopus 로고
    • Flexible temporal expression profile modelling using the Gaussian process
    • 10.1016/j.csda.2005.11.017, 3095810, 21617730
    • Yuan M. Flexible temporal expression profile modelling using the Gaussian process. Computational statistics & data analysis 2006, 51(3):1754-1764. 10.1016/j.csda.2005.11.017, 3095810, 21617730.
    • (2006) Computational statistics & data analysis , vol.51 , Issue.3 , pp. 1754-1764
    • Yuan, M.1
  • 24
    • 65549161909 scopus 로고    scopus 로고
    • Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data
    • 10.1093/bioinformatics/btp139, 2677737, 19289448
    • Kirk PDW, Stumpf MPH. Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinformatics 2009, 25(10):1300. 10.1093/bioinformatics/btp139, 2677737, 19289448.
    • (2009) Bioinformatics , vol.25 , Issue.10 , pp. 1300
    • Kirk, P.D.W.1    Stumpf, M.P.H.2
  • 26
    • 49549105346 scopus 로고    scopus 로고
    • Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities
    • 10.1093/bioinformatics/btn278, 18689843
    • Gao P, Honkela A, Rattray M, Lawrence ND. Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities. Bioinformatics 2008, 24(16):i70. 10.1093/bioinformatics/btn278, 18689843.
    • (2008) Bioinformatics , vol.24 , Issue.16
    • Gao, P.1    Honkela, A.2    Rattray, M.3    Lawrence, N.D.4
  • 28
    • 27844592624 scopus 로고    scopus 로고
    • Variational inference for Student-t models: Robust Bayesian interpolation and generalised component analysis
    • Tipping ME, Lawrence ND. Variational inference for Student-t models: Robust Bayesian interpolation and generalised component analysis. Neurocomputing 2005, 69(1-3):123-141.
    • (2005) Neurocomputing , vol.69 , Issue.1-3 , pp. 123-141
    • Tipping, M.E.1    Lawrence, N.D.2
  • 30
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249, 12925520
    • Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249. 10.1093/biostatistics/4.2.249, 12925520.
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5    Scherf, U.6    Speed, T.P.7
  • 32
    • 0027205884 scopus 로고
    • A scaled conjugate gradient algorithm for fast supervised learning
    • Möller MF. A scaled conjugate gradient algorithm for fast supervised learning. Neural networks 1993, 6(4):525-533.
    • (1993) Neural networks , vol.6 , Issue.4 , pp. 525-533
    • Möller, M.F.1
  • 33
    • 0000597408 scopus 로고    scopus 로고
    • Comparison of approximate methods for handling hyperparameters
    • MacKay DJC. Comparison of approximate methods for handling hyperparameters. Neural Computation 1999, 11(5):1035-1068.
    • (1999) Neural Computation , vol.11 , Issue.5 , pp. 1035-1068
    • MacKay, D.J.C.1
  • 34
    • 0004220749 scopus 로고    scopus 로고
    • Monte Carlo implementation of Gaussian process models for Bayesian regression and classification
    • Neal RM. Monte Carlo implementation of Gaussian process models for Bayesian regression and classification. Arxiv preprint physics/9701026 1997,
    • (1997) Arxiv preprint physics/9701026
    • Neal, R.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.