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Volumn 8, Issue , 2007, Pages

Including probe-level uncertainty in model-based gene expression clustering

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL VARIATION; EXPRESSION PATTERNS; GAUSSIAN MIXTURE MODEL; GENE EXPRESSION CLUSTERING; GENE EXPRESSION DATA; MICROARRAY EXPERIMENTS; MICROARRAY GENE EXPRESSION DATA; MODEL-BASED CLUSTERING;

EID: 34147152900     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-98     Document Type: Article
Times cited : (21)

References (37)
  • 1
    • 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 467-470 10.1126/science.270.5235.467 7569999
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 0036899286 scopus 로고    scopus 로고
    • From pattern to pathways: Gene expression data analysis comes of age
    • 10.1038/ng1033 12454645
    • Slonim DK From pattern to pathways: Gene expression data analysis comes of age Nature Genetics 2002 32 Suppl 502-508 10.1038/ng1033 12454645
    • (2002) Nature Genetics , vol.32 , Issue.SUPPL. , pp. 502-508
    • Slonim, D.K.1
  • 4
    • 0035375137 scopus 로고    scopus 로고
    • Computational Analysis of Microarray Data
    • 10.1038/35076576 11389458
    • Quackenbush J Computational Analysis of Microarray Data Nature Reviews Genetics 2001 2 418-427 10.1038/35076576 11389458
    • (2001) Nature Reviews Genetics , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 5
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • 24541 10.1073/pnas.95.25.14863 9843981
    • Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998 95 14863-14868 24541 9843981 10.1073/pnas.95.25.14863
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 6
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • 10.1038/10343 10391217
    • Tavazoie S Hughes JD Campbell MJ Cho RJ Church GM Systematic determination of genetic network architecture Nat Genet 1999 22 281-285 10.1038/10343 10391217
    • (1999) Nat Genet , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.D.2    Campbell, M.J.3    Cho, R.J.4    Church, G.M.5
  • 7
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression withself-organizing maps: Methods and application to hematopoietic differentiation
    • 10.1073/pnas.96.6.2907
    • Tamayo P Slonim D Mesirov J Zhu Q Kitareewan S Dmitrovsky E Lander ES Golub TR Interpreting patterns of gene expression withself-organizing maps: Methods and application to hematopoietic differentiation Proc Natl Acad Sci USA 1999 22 2907-2912 10.1073/pnas.96.6.2907
    • (1999) Proc Natl Acad Sci USA , vol.22 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 8
    • 28644449917 scopus 로고    scopus 로고
    • How does gene expression clustering work?
    • 10.1038/nbt1205-1499 16333293
    • D'haeseleer P How does gene expression clustering work? Nature Biotechnology 2005 23 1499-1501 10.1038/nbt1205-1499 16333293
    • (2005) Nature Biotechnology , vol.23 , pp. 1499-1501
    • D'haeseleer, P.1
  • 9
    • 0035998835 scopus 로고    scopus 로고
    • Model-based clustering, discriminant analysis and density estimation
    • 10.1198/016214502760047131
    • Fraley C Raftery AE Model-based clustering, discriminant analysis and density estimation J Am Stat Assoc 2002 97 911-931 10.1198/ 016214502760047131
    • (2002) J Am Stat Assoc , vol.97 , pp. 911-931
    • Fraley, C.1    Raftery, A.E.2
  • 10
    • 0034782618 scopus 로고    scopus 로고
    • Model-based clustering and data transformations for gene expression data
    • 10.1093/bioinformatics/17.10.977 11673243
    • Yeung KY Fraley C Murua A Raftery AE Ruzzo WL Model-based clustering and data transformations for gene expression data Bioinformatics 2001 17 10 977-987 10.1093/bioinformatics/17.10.977 11673243
    • (2001) Bioinformatics , vol.17 , Issue.10 , pp. 977-987
    • Yeung, K.Y.1    Fraley, C.2    Murua, A.3    Raftery, A.E.4    Ruzzo, W.L.5
  • 11
    • 4444237023 scopus 로고    scopus 로고
    • A comparison of cluster analysis methods using DNA methylation data
    • 10.1093/bioinformatics/bth176 15044245
    • Siegmund KD Laird PW Laird-Offringa IA A comparison of cluster analysis methods using DNA methylation data Bioinformatics 2004 20 1896-1904 10.1093/bioinformatics/bth176 15044245
    • (2004) Bioinformatics , vol.20 , pp. 1896-1904
    • Siegmund, K.D.1    Laird, P.W.2    Laird-Offringa, I.A.3
  • 12
    • 8644265125 scopus 로고    scopus 로고
    • Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance
    • 10.1073/pnas.0407114101
    • Lin KK Chudova D Hatfield GW Smyth P Andersen B Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance Proceedings of the National Academy of Science USA 2004 101 15955-15960 10.1073/pnas.0407114101
    • (2004) Proceedings of the National Academy of Science USA , vol.101 , pp. 15955-15960
    • Lin, K.K.1    Chudova, D.2    Hatfield, G.W.3    Smyth, P.4    Andersen, B.5
  • 14
    • 17744413236 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application
    • 55329 research0032 11532216
    • Li C Wong WH Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application Genome Biology 2001 2 8 research0032 55329 11532216
    • (2001) Genome Biology , vol.2 , Issue.8
    • Li, C.1    Wong, W.H.2
  • 16
    • 27544443176 scopus 로고    scopus 로고
    • Accounting for probe-level noise in principal component analysis of microarray data
    • 10.1093/bioinformatics/bti617 16091409
    • Sanguinetti G Milo M Rattray M Lawrence ND Accounting for probe-level noise in principal component analysis of microarray data Bioinformatics 2005 21 3748-3754 10.1093/bioinformatics/bti617 16091409
    • (2005) Bioinformatics , vol.21 , pp. 3748-3754
    • Sanguinetti, G.1    Milo, M.2    Rattray, M.3    Lawrence, N.D.4
  • 17
    • 33748644662 scopus 로고    scopus 로고
    • Probe-level measurement error improves accuracy in detecting differential gene expression
    • 10.1093/bioinformatics/btl361 16820429
    • Liu X Milo M Lawrence ND Rattray M Probe-level measurement error improves accuracy in detecting differential gene expression Bioinformatics 2006 22 2107-2113 10.1093/bioinformatics/btl361 16820429
    • (2006) Bioinformatics , vol.22 , pp. 2107-2113
    • Liu, X.1    Milo, M.2    Lawrence, N.D.3    Rattray, M.4
  • 18
    • 24644460573 scopus 로고    scopus 로고
    • A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
    • 10.1093/bioinformatics/bti583 16020470
    • Liu X Milo M Lawrence ND Rattray M A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips Bioinformatics 2005 21 18 3637-3644 10.1093/bioinformatics/bti583 16020470
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3637-3644
    • Liu, X.1    Milo, M.2    Lawrence, N.D.3    Rattray, M.4
  • 19
    • 84886762846 scopus 로고    scopus 로고
    • PUMA - Propagating Uncertainty in Microarray Analysis
    • PUMA - Propagating Uncertainty in Microarray Analysis http://www.bioinf.manchester.ac.uk/resources/puma/
  • 20
    • 22844453564 scopus 로고    scopus 로고
    • Mclust: Software for model-based cluster analysis
    • 10.1007/s003579900058
    • Fraley C Raftery AE Mclust: Software for model-based cluster analysis J Classification 2002 16 297-306 10.1007/s003579900058
    • (2002) J Classification , vol.16 , pp. 297-306
    • Fraley, C.1    Raftery, A.E.2
  • 21
    • 84948872101 scopus 로고
    • A study of the comparability of external criteria for hierarchical cluster analysis
    • 10.1207/s15327906mbr2104_5
    • Milligan GW Cooper MC A study of the comparability of external criteria for hierarchical cluster analysis Multivariate Behavioral Research 1986 21 441-458 10.1207/s15327906mbr2104_5
    • (1986) Multivariate Behavioral Research , vol.21 , pp. 441-458
    • Milligan, G.W.1    Cooper, M.C.2
  • 23
    • 0037667290 scopus 로고    scopus 로고
    • Clustering gene-expression data with repeated measurements
    • 156590 12734014 10.1186/gb-2003-4-5-r34
    • Yeung KY Medvedovic M Bumgarner RE Clustering gene-expression data with repeated measurements Genome Biology 2003 4 R34 156590 12734014 10.1186/ gb-2003-4-5-r34
    • (2003) Genome Biology , vol.4 , Issue.4
    • Yeung, K.Y.1    Medvedovic, M.2    Bumgarner, R.E.3
  • 24
    • 0037399775 scopus 로고    scopus 로고
    • Cluster validation techniques for genome expression data
    • 10.1016/S0165-1684(02)00475-9
    • Bolshakova N Azuaje F Cluster validation techniques for genome expression data Signal Process 2003 83 825-833 10.1016/ S0165-1684(02)00475-9
    • (2003) Signal Process , vol.83 , pp. 825-833
    • Bolshakova, N.1    Azuaje, F.2
  • 25
    • 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
  • 26
    • 27944487902 scopus 로고    scopus 로고
    • Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
    • 10.1126/science.1120499 16254148
    • Tu BP Kudlicki A Rowicka M McKnight SL Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes Science 2005 310 1152-1158 10.1126/science.1120499 16254148
    • (2005) Science , vol.310 , pp. 1152-1158
    • Tu, B.P.1    Kudlicki, A.2    Rowicka, M.3    McKnight, S.L.4
  • 28
    • 0034948896 scopus 로고    scopus 로고
    • A Baysian framework for the analysis of microarray expression data: Regularized t-test and statistical infrence of gene changes
    • 10.1093/bioinformatics/17.6.509 11395427
    • Baldi P Long AD A Baysian framework for the analysis of microarray expression data: Regularized t-test and statistical infrence of gene changes Bioinformatics 2001 17 509-519 10.1093/bioinformatics/17.6.509 11395427
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 29
    • 84873304111 scopus 로고    scopus 로고
    • Gene Expression Omnibus, accession number GDS912
    • Gene Expression Omnibus, accession number GDS912 http://www.ncbi.nlm.nih.gov/projects/geo/
  • 31
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwartz G Estimating the dimension of a model Ann Stat 1978 6 461-464
    • (1978) Ann Stat , vol.6 , pp. 461-464
    • Schwartz, G.1
  • 32
    • 0242291493 scopus 로고    scopus 로고
    • MCLUST: Software for Model-Based Clustering, Discriminant Analysis and Density Estimation
    • Department of Statistics, University of Washington
    • Fraley C Raftery AE MCLUST: Software for Model-Based Clustering, Discriminant Analysis and Density Estimation Tech Rep 415R Department of Statistics, University of Washington 2002
    • (2002) Tech Rep 415R
    • Fraley, C.1    Raftery, A.E.2
  • 35
    • 0027453616 scopus 로고
    • Model-based Gaussian and non-Gaussian clustering
    • 10.2307/2532201
    • Banfield JD Raftery AE Model-based Gaussian and non-Gaussian clustering Biometrics 1993 49 803-821 10.2307/2532201
    • (1993) Biometrics , vol.49 , pp. 803-821
    • Banfield, J.D.1    Raftery, A.E.2
  • 36
    • 0036433588 scopus 로고    scopus 로고
    • SNOPT: An SQP algorithm for large-scale constrained optimization
    • 10.1137/S1052623499350013
    • Gill PE Murray W Saunders MA SNOPT: An SQP algorithm for large-scale constrained optimization SIAM Journal on Optimization 2002 12 979-1006 10.1137/S1052623499350013
    • (2002) SIAM Journal on Optimization , vol.12 , pp. 979-1006
    • Gill, P.E.1    Murray, W.2    Saunders, M.A.3
  • 37
    • 0001346976 scopus 로고    scopus 로고
    • A SQP method for general nonlinear programs using only equality constrained subproblems
    • Spellucci PA A SQP method for general nonlinear programs using only equality constrained subproblems Mathematical Programming 1998 82 413-448
    • (1998) Mathematical Programming , vol.82 , pp. 413-448
    • Spellucci, P.A.1


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