메뉴 건너뛰기




Volumn 14, Issue 4, 2013, Pages 423-436

Accounting for noise when clustering biological data

Author keywords

Cluster ensemble; Clustering; Measurement variability; Noise; Random effects; Unsupervised learning

Indexed keywords

PROTEIN; TRANSCRIPTOME;

EID: 84889028394     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs057     Document Type: Article
Times cited : (24)

References (38)
  • 2
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie S, Hughes JD, Campbell MJ, et al. Systematic determination of genetic network architecture. America 1999;22:281-5.
    • (1999) America , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.D.2    Campbell, M.J.3
  • 3
    • 66349135301 scopus 로고    scopus 로고
    • Application of fuzzy c-means clustering in data analysis of metabolomics
    • Li X, Lu X, Tian J, et al. Application of fuzzy c-means clustering in data analysis of metabolomics. Anal Chem 2009;81(11):4468-75.
    • (2009) Anal Chem , vol.81 , Issue.11 , pp. 4468-4475
    • Li, X.1    Lu, X.2    Tian, J.3
  • 4
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
    • Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286(5439):531-7.
    • (1999) Science , vol.286 , Issue.5439 , pp. 531-537
    • Golub, T.R.1    Slonim, D.K.2    Tamayo, P.3
  • 5
    • 33750696663 scopus 로고    scopus 로고
    • Effects of HER2 overexpression on cell signaling networks governing proliferation and migration
    • Wolf-Yadlin A, Kumar N, Zhang Y, et al. Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol 2006;2:54.
    • (2006) Mol Syst Biol , vol.2 , pp. 54
    • Wolf-Yadlin, A.1    Kumar, N.2    Zhang, Y.3
  • 6
    • 0141626917 scopus 로고    scopus 로고
    • The effect of replication on gene expression microarray experiments
    • Pavlidis P, Li Q, Noble WS. The effect of replication on gene expression microarray experiments. Bioinformatics 2003;19(13):1620-7.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1620-1627
    • Pavlidis, P.1    Li, Q.2    Noble, W.S.3
  • 7
    • 0034730124 scopus 로고    scopus 로고
    • Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations
    • Lee ML, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000;97(18):9834-9.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.18 , pp. 9834-9839
    • Lee, M.L.1    Kuo, F.C.2    Whitmore, G.A.3    Sklar, J.4
  • 8
    • 0036207548 scopus 로고    scopus 로고
    • Inference from clustering with application to gene-expression microarrays
    • Dougherty ER, Barrera J, Brun M, et al. Inference from clustering with application to gene-expression microarrays. JComputBiol 2002;9(1):105-26.
    • (2002) JComputBiol , vol.9 , Issue.1 , pp. 105-126
    • Dougherty, E.R.1    Barrera, J.2    Brun, M.3
  • 9
    • 3042686005 scopus 로고    scopus 로고
    • Bayesian mixture model based clustering of replicated microarray data
    • Medvedovic M, Yeung K, Bumgarner R. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics 2004;20(8):1222-32.
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1222-1232
    • Medvedovic, M.1    Yeung, K.2    Bumgarner, R.3
  • 10
    • 33747890494 scopus 로고    scopus 로고
    • A mixture model with random-effects components for clustering correlated gene-expression profiles
    • Ng SK, McLachlan GJ, Wang K, et al. A mixture model with random-effects components for clustering correlated gene-expression profiles. Bioinformatics 2006;22(14):1745-52.
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1745-1752
    • Ng, S.K.1    McLachlan, G.J.2    Wang, K.3
  • 11
    • 80053928843 scopus 로고    scopus 로고
    • Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements
    • Cooke EJ, Savage RS, Kirk PDW, et al. Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. BMC Bioinformatics 2011;12(1):399.
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 399
    • Cooke, E.J.1    Savage, R.S.2    Kirk, P.D.W.3
  • 12
    • 0037667290 scopus 로고    scopus 로고
    • Clustering gene-expression data with repeated measurements
    • R34
    • Yeung KY, Medvedovic M, Bumgarner RE. Clustering gene-expression data with repeated measurements. Genome Biol 2003;4(5):R34:1-17.
    • (2003) Genome Biol , vol.4 , Issue.5 , pp. 1-17
    • Yeung, K.Y.1    Medvedovic, M.2    Bumgarner, R.E.3
  • 13
    • 0035979259 scopus 로고    scopus 로고
    • Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments
    • Kerr MK, Churchill GA. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. ProcNatl Acad SciUSA 2001;98(16):8961-5.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.16 , pp. 8961-8965
    • Kerr, M.K.1    Churchill, G.A.2
  • 14
    • 0034601455 scopus 로고    scopus 로고
    • Molecular classification of cutaneous malignant melanoma by gene expression profiling
    • Bittner M, Meltzer P, Chen Y, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000;406:536-40.
    • (2000) Nature , vol.406 , pp. 536-540
    • Bittner, M.1    Meltzer, P.2    Chen, Y.3
  • 16
    • 0041965980 scopus 로고    scopus 로고
    • Cluster ensembles-a knowledge reuse framework for combining multiple partitions
    • Strehl A, Gosh J. Cluster ensembles-a knowledge reuse framework for combining multiple partitions. J Machine LearnRes 2002;3:583-617.
    • (2002) J Machine Learn Res , vol.3 , pp. 583-617
    • Strehl, A.1    Gosh, J.2
  • 17
  • 18
    • 30344442460 scopus 로고    scopus 로고
    • Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm
    • Grotkjaer T, Winther O, Regenberg B, et al. Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. Bioinformatics 2006;22(1):58-67.
    • (2006) Bioinformatics , vol.22 , Issue.1 , pp. 58-67
    • Grotkjaer, T.1    Winther, O.2    Regenberg, B.3
  • 19
    • 0038724494 scopus 로고    scopus 로고
    • Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data
    • Monti S, Tamayo P, Mesirov J, Golub T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Machine Learn 2003;52:91-118.
    • (2003) Machine Learn , vol.52 , pp. 91-118
    • Monti, S.1    Tamayo, P.2    Mesirov, J.3    Golub, T.4
  • 21
    • 33947159574 scopus 로고    scopus 로고
    • Evaluation of stability of k-means cluster ensembles with respect to random initialization
    • Kuncheva LI, Vetrov DP. Evaluation of stability of k-means cluster ensembles with respect to random initialization. IEEETrans PatternAnalMachine Intell 2006;28(11):1798-808.
    • (2006) IEEE Trans Pattern Anal Machine Intell , vol.28 , Issue.11 , pp. 1798-1808
    • Kuncheva, L.I.1    Vetrov, D.P.2
  • 22
    • 79960956222 scopus 로고    scopus 로고
    • MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets
    • Naegle KM, Welsch RE, Yaffe MB, et al. MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS Comput Biol 2011;7(7):e1002119.
    • (2011) PLoS Comput Biol , vol.7 , Issue.7
    • Naegle, K.M.1    Welsch, R.E.2    Yaffe, M.B.3
  • 23
    • 77952482885 scopus 로고    scopus 로고
    • Multi-level bootstrap analysis of stable clusters in resting-state fMRI
    • Bellec P, Rosa-Neto P, Lyttelton OC, et al. Multi-level bootstrap analysis of stable clusters in resting-state fMRI. NeuroImage 2010;51(3):1126-39.
    • (2010) Neuro Image , vol.51 , Issue.3 , pp. 1126-1139
    • Bellec, P.1    Rosa-Neto, P.2    Lyttelton, O.C.3
  • 24
    • 77958118466 scopus 로고    scopus 로고
    • Link CluE: A MATLAB package for link-based cluster ensembles
    • Iam-on N, Garrett S. LinkCluE: A MATLAB package for link-based cluster ensembles. J Stat Software 2010;36(9):1-36.
    • (2010) J Stat Software , vol.36 , Issue.9 , pp. 1-36
    • Iam-on, N.1    Garrett, S.2
  • 25
    • 61449214257 scopus 로고    scopus 로고
    • Fuzzy ensemble clustering based on random projections for DNA microarray data analysis
    • Avogadri R, Valentini G. Fuzzy ensemble clustering based on random projections for DNA microarray data analysis. Artif IntellMed 2009;45(2-3):173-83.
    • (2009) Artif Intell Med , vol.45 , Issue.2-3 , pp. 173-183
    • Avogadri, R.1    Valentini, G.2
  • 26
    • 80054920244 scopus 로고    scopus 로고
    • CLICOM: Cliques for combining multiple clusterings
    • Mimaroglu S, Yagci M. CLICOM: Cliques for combining multiple clusterings. Expert Syst Appl 2012;39:1889-901.
    • (2012) Expert Syst Appl , vol.39 , pp. 1889-1901
    • Mimaroglu, S.1    Yagci, M.2
  • 27
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes
    • Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001;17(6):509-19.
    • (2001) Bioinformatics , vol.17 , Issue.6 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 29
    • 79952579286 scopus 로고    scopus 로고
    • Biological assessment of robust noise models in microarray data analysis
    • Posekany A, Felsenstein K, Sykacek P. Biological assessment of robust noise models in microarray data analysis. Bioinformatics 2011;27(6):807-14.
    • (2011) Bioinformatics , vol.27 , Issue.6 , pp. 807-814
    • Posekany, A.1    Felsenstein, K.2    Sykacek, P.3
  • 30
    • 0042093637 scopus 로고    scopus 로고
    • Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays
    • Draghici S, Kulaeva O, Hoff B, et al. Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays. Bioinformatics 2003;19(11):1348-59.
    • (2003) Bioinformatics , vol.19 , Issue.11 , pp. 1348-1359
    • Draghici, S.1    Kulaeva, O.2    Hoff, B.3
  • 31
    • 33749332751 scopus 로고    scopus 로고
    • Temporal dynamics of tyrosine phosphorylation in insulin signaling
    • Schmelzle K, Kane S, Gridley S, etal. Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 2006;55:2171-9.
    • (2006) Diabetes , vol.55 , pp. 2171-2179
    • Schmelzle, K.1    Kane, S.2    Gridley, S.3
  • 32
    • 78149309682 scopus 로고    scopus 로고
    • PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies
    • Naegle KM, Gymrek M, Joughin BA, et al. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics 2010;9(11):2558-70.
    • (2010) Mol Cell Proteomics , vol.9 , Issue.11 , pp. 2558-2570
    • Naegle, K.M.1    Gymrek, M.2    Joughin, B.A.3
  • 33
    • 34047174559 scopus 로고    scopus 로고
    • A module of negative feedback regulators defines growth factor signaling
    • Amit I, Citri A, Shay T, etal. A module of negative feedback regulators defines growth factor signaling. Nat Genet 2007;39(4):503-12.
    • (2007) Nat Genet , vol.39 , Issue.4 , pp. 503-512
    • Amit, I.1    Citri, A.2    Shay, T.3
  • 34
    • 1542405872 scopus 로고    scopus 로고
    • Pharmacogenomic identification of targets for adjuvant therapy with the topoisomerase poison camptothecin
    • Carson JP, Zhang N, Frampton GM, et al. Pharmacogenomic identification of targets for adjuvant therapy with the topoisomerase poison camptothecin. Cancer Res 2004;64(6):2096-104.
    • (2004) Cancer Res , vol.64 , Issue.6 , pp. 2096-2104
    • Carson, J.P.1    Zhang, N.2    Frampton, G.M.3
  • 35
    • 34547838641 scopus 로고    scopus 로고
    • The abundance of rnps1, a protein component of the exon junction complex, can determine the variability in efficiency of the nonsense mediated decay pathway
    • Viegas MH, Gehring NH, Breit S, et al. The abundance of rnps1, a protein component of the exon junction complex, can determine the variability in efficiency of the nonsense mediated decay pathway. Nucleic Acids Res 2007;35(13):4542-51.
    • (2007) Nucleic Acids Res , vol.35 , Issue.13 , pp. 4542-4551
    • Viegas, M.H.1    Gehring, N.H.2    Breit, S.3
  • 36
    • 0344703599 scopus 로고    scopus 로고
    • Normality of oligonucleotide microarray data and implications for parametric statistical analyses
    • Giles PJ, Kipling D. Normality of oligonucleotide microarray data and implications for parametric statistical analyses. Bioinformatics 2003;19(17):2254-62.
    • (2003) Bioinformatics , vol.19 , Issue.17 , pp. 2254-2262
    • Giles, P.J.1    Kipling, D.2
  • 37
    • 0037195138 scopus 로고    scopus 로고
    • Quantitative noise analysis for gene expression microarray experiments
    • Tu Y, Stolovitzky G, Klein U. Quantitative noise analysis for gene expression microarray experiments. Proc Natl Acad Sci USA 2002;99(22):14031-6.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.22 , pp. 14031-14036
    • Tu, Y.1    Stolovitzky, G.2    Klein, U.3
  • 38
    • 70149109457 scopus 로고    scopus 로고
    • A note on oligonucleotide expression values not being normally distributed
    • Hardin J, Wilson J. A note on oligonucleotide expression values not being normally distributed. Biostatistics 2009;10(3):446-50.
    • (2009) Biostatistics , vol.10 , Issue.3 , pp. 446-450
    • Hardin, J.1    Wilson, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.