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Volumn 10, Issue , 2009, Pages 358-

ArrayMining: A modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Author keywords

[No Author keywords available]

Indexed keywords

CONSENSUS CLUSTERING; ENSEMBLE FEATURE SELECTIONS; ENSEMBLE PREDICTION; FUNCTIONAL ANNOTATION; MICROARRAY ANALYSIS; MULTIPLE ALGORITHMS; NORMALIZATION METHODS; SAMPLE CLASSIFICATION;

EID: 70849131666     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-358     Document Type: Article
Times cited : (92)

References (56)
  • 3
    • 0030305457 scopus 로고    scopus 로고
    • R: A Language for Data Analysis and Graphics
    • Ihaka R, Gentleman R. R: A Language for Data Analysis and Graphics. J Comput Graph Stat 1996, 5(3):299-314.
    • (1996) J Comput Graph Stat , vol.5 , Issue.3 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 7
    • 34547598395 scopus 로고    scopus 로고
    • Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
    • 1933128, 17488846
    • Diaz-Uriarte R, Alibes A, Morrissey E. Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. Nucleic Acids Res 2007, (35 Web Server):W75. 1933128, 17488846.
    • (2007) Nucleic Acids Res , vol.Web Server , Issue.35
    • Diaz-Uriarte, R.1    Alibes, A.2    Morrissey, E.3
  • 8
    • 40549091953 scopus 로고    scopus 로고
    • EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
    • 2265266, 18218103
    • Zhu Y, Zhu Y, Xu W. EzArray: A web-based highly automated Affymetrix expression array data management and analysis system. BMC Bioinformatics 2008, 9:46. 2265266, 18218103.
    • (2008) BMC Bioinformatics , vol.9 , pp. 46
    • Zhu, Y.1    Zhu, Y.2    Xu, W.3
  • 9
    • 33747839466 scopus 로고    scopus 로고
    • CARMAweb: comprehensive R-and bioconductor-based web service for microarray data analysis
    • 1538903, 16845058
    • Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z. CARMAweb: comprehensive R-and bioconductor-based web service for microarray data analysis. Nucleic Acids Res 2006, (34 Web Server):W498. 1538903, 16845058.
    • (2006) Nucleic Acids Res , vol.Web Server , Issue.34
    • Rainer, J.1    Sanchez-Cabo, F.2    Stocker, G.3    Sturn, A.4    Trajanoski, Z.5
  • 10
    • 34547579397 scopus 로고    scopus 로고
    • MAGMA: analysis of two-channel microarrays made easy
    • 1933123, 17517778
    • Rehrauer H, Zoller S, Schlapbach R. MAGMA: analysis of two-channel microarrays made easy. Nucleic Acids Research 2007, (35 Web Server):W86. 1933123, 17517778.
    • (2007) Nucleic Acids Research , vol.Web Server , Issue.35
    • Rehrauer, H.1    Zoller, S.2    Schlapbach, R.3
  • 12
    • 23144446164 scopus 로고    scopus 로고
    • RACE: remote analysis computation for gene expression data
    • 1160250, 15980552
    • Psarros M, Heber S, Sick M, Thoppae G, Harshman K, Sick B. RACE: remote analysis computation for gene expression data. Nucleic Acids Res 2005, (33 Web Server):W638. 1160250, 15980552.
    • (2005) Nucleic Acids Res , vol.Web Server , Issue.33
    • Psarros, M.1    Heber, S.2    Sick, M.3    Thoppae, G.4    Harshman, K.5    Sick, B.6
  • 13
    • 30044444274 scopus 로고    scopus 로고
    • WebArray: an online platform for microarray data analysis
    • 1327694, 16371165
    • Xia X, McClelland M, Wang Y. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 2005, 6:306. 1327694, 16371165.
    • (2005) BMC Bioinformatics , vol.6 , pp. 306
    • Xia, X.1    McClelland, M.2    Wang, Y.3
  • 14
    • 23144442350 scopus 로고    scopus 로고
    • MIDAW: a web tool for statistical analysis of microarray data
    • 1160257, 15980553
    • Romualdi C, Vitulo N, Favero M, Lanfranchi G. MIDAW: a web tool for statistical analysis of microarray data. Nucleic Acids Res 2005, (33 Web Server):W644. 1160257, 15980553.
    • (2005) Nucleic Acids Res , vol.Web Server , Issue.33
    • Romualdi, C.1    Vitulo, N.2    Favero, M.3    Lanfranchi, G.4
  • 15
    • 17244373571 scopus 로고    scopus 로고
    • Gene expression module discovery using Gibbs sampling
    • Wu C, Fu Y, Murali T, Kasif S. Gene expression module discovery using Gibbs sampling. Genome Inform 2004, 15:239-248.
    • (2004) Genome Inform , vol.15 , pp. 239-248
    • Wu, C.1    Fu, Y.2    Murali, T.3    Kasif, S.4
  • 16
    • 33745062476 scopus 로고    scopus 로고
    • Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
    • 1479375, 16670020
    • Lee J, Sinkovits R, Mock D, Rab E, Cai J, Yang P, Saunders B, Hsueh R, Choi S, Subramaniam S. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics 2006, 7:237. 1479375, 16670020.
    • (2006) BMC Bioinformatics , vol.7 , pp. 237
    • Lee, J.1    Sinkovits, R.2    Mock, D.3    Rab, E.4    Cai, J.5    Yang, P.6    Saunders, B.7    Hsueh, R.8    Choi, S.9    Subramaniam, S.10
  • 17
    • 23144445453 scopus 로고    scopus 로고
    • ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
    • 1160207, 15980557
    • Aburatani S, Goto K, Saito S, Toh H, Horimoto K. ASIAN: a web server for inferring a regulatory network framework from gene expression profiles. Nucleic Acids Res 2005, (33 Web Server):W659. 1160207, 15980557.
    • (2005) Nucleic Acids Res , vol.Web Server , Issue.33
    • Aburatani, S.1    Goto, K.2    Saito, S.3    Toh, H.4    Horimoto, K.5
  • 18
    • 34547582422 scopus 로고    scopus 로고
    • Cross-species microarray analysis with the OSCAR system suggests an INSR -> Pax6 -> NQO1 neuro-protective pathway in aging and Alzheimer's disease
    • 1933158, 17545194
    • Lu Y, He X, Zhong S. Cross-species microarray analysis with the OSCAR system suggests an INSR -> Pax6 -> NQO1 neuro-protective pathway in aging and Alzheimer's disease. Nucleic Acids Res 2007, (35 Web Server):W105. 1933158, 17545194.
    • (2007) Nucleic Acids Res , vol.Web Server , Issue.35
    • Lu, Y.1    He, X.2    Zhong, S.3
  • 20
    • 2942596534 scopus 로고    scopus 로고
    • Ensemble machine learning on gene expression data for cancer classification
    • Tan A, Gilbert D. Ensemble machine learning on gene expression data for cancer classification. Appl Bioinformatics 2003, 2(3 Suppl):S75-S83.
    • (2003) Appl Bioinformatics , vol.2 Suppl , Issue.3
    • Tan, A.1    Gilbert, D.2
  • 21
    • 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 Learning 2003, 52:91-118.
    • (2003) Machine Learning , vol.52 , pp. 91-118
    • Monti, S.1    Tamayo, P.2    Mesirov, J.3    Golub, T.4
  • 22
    • 24944539029 scopus 로고    scopus 로고
    • Consensus clustering and functional interpretation of gene-expression data
    • 545785, 15535870
    • Swift S, Tucker A, Vinciotti V, Martin N, Orengo C, Liu X, Kellam P. Consensus clustering and functional interpretation of gene-expression data. Genome Biol 2004, 5(11):R94. 545785, 15535870.
    • (2004) Genome Biol , vol.5 , Issue.11
    • Swift, S.1    Tucker, A.2    Vinciotti, V.3    Martin, N.4    Orengo, C.5    Liu, X.6    Kellam, P.7
  • 23
    • 42649134796 scopus 로고    scopus 로고
    • Merging two gene-expression studies via cross-platform normalization
    • Shabalin A, Tjelmeland H, Fan C, Perou C, Nobel A. Merging two gene-expression studies via cross-platform normalization. Bioinformatics 2008, 24(9):1154.
    • (2008) Bioinformatics , vol.24 , Issue.9 , pp. 1154
    • Shabalin, A.1    Tjelmeland, H.2    Fan, C.3    Perou, C.4    Nobel, A.5
  • 24
    • 27844594381 scopus 로고    scopus 로고
    • Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
    • 1312314, 16271137
    • Warnat P, Eils R, Brors B. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics 2005, 6:265. 1312314, 16271137.
    • (2005) BMC Bioinformatics , vol.6 , pp. 265
    • Warnat, P.1    Eils, R.2    Brors, B.3
  • 25
    • 84888286827 scopus 로고    scopus 로고
    • VRMLGen R software package
    • VRMLGen R software package. , http://bree.cs.nott.ac.uk/vrmlgen
  • 27
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • 99122, 11752295
    • Edgar R, Domrachev M, Lash A. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210. 99122, 11752295.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.3
  • 29
    • 55249088991 scopus 로고    scopus 로고
    • Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients
    • 2576259, 18937867
    • Walker W, Liao I, Gilbert D, Wong B, Pollard K, McCulloch C, Lit L, Sharp F. Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics 2008, 9:494. 2576259, 18937867.
    • (2008) BMC Genomics , vol.9 , pp. 494
    • Walker, W.1    Liao, I.2    Gilbert, D.3    Wong, B.4    Pollard, K.5    McCulloch, C.6    Lit, L.7    Sharp, F.8
  • 31
    • 0036012343 scopus 로고    scopus 로고
    • Replicated microarray data
    • Lonnstedt I, Speed T. Replicated microarray data. Stat Sin 2002, 12:31-46.
    • (2002) Stat Sin , vol.12 , pp. 31-46
    • Lonnstedt, I.1    Speed, T.2
  • 32
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • 16646809
    • Smyth G. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:3. 16646809.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 3
    • Smyth, G.1
  • 33
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • 33173, 11309499
    • Tusher V, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(9):5116-5121. 33173, 11309499.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.9 , pp. 5116-5121
    • Tusher, V.1    Tibshirani, R.2    Chu, G.3
  • 35
  • 36
    • 33846515112 scopus 로고    scopus 로고
    • Partial least squares: a versatile tool for the analysis of high-dimensional genomic data
    • Boulesteix A, Strimmer K. Partial least squares: a versatile tool for the analysis of high-dimensional genomic data. Brief Bioinform 2007, 8:32-44.
    • (2007) Brief Bioinform , vol.8 , pp. 32-44
    • Boulesteix, A.1    Strimmer, K.2
  • 38
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • 124443, 12011421
    • Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002, 99(10):6567-6572. 124443, 12011421.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.10 , pp. 6567-6572
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 40
    • 0035108235 scopus 로고    scopus 로고
    • A hierarchical unsupervised growing neural network for clustering gene expression patterns
    • Herrero J, Valencia A, Dopazo J. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 2001, 17(2):126-136.
    • (2001) Bioinformatics , vol.17 , Issue.2 , pp. 126-136
    • Herrero, J.1    Valencia, A.2    Dopazo, J.3
  • 41
    • 33645579248 scopus 로고    scopus 로고
    • Hybrid hierarchical clustering with applications to microarray data
    • Chipman H, Tibshirani R. Hybrid hierarchical clustering with applications to microarray data. Biostatistics 2006, 7(2):286-301.
    • (2006) Biostatistics , vol.7 , Issue.2 , pp. 286-301
    • Chipman, H.1    Tibshirani, R.2
  • 42
    • 0002964209 scopus 로고
    • Fast simulated annealing
    • Szu H. Fast simulated annealing. AIP Conference Proceedings 1986, 151:420.
    • (1986) AIP Conference Proceedings , vol.151 , pp. 420
    • Szu, H.1
  • 43
    • 38949177447 scopus 로고    scopus 로고
    • ProCKSI: A decision support system for protein (structure) comparison, knowledge, similarity and information
    • 2222653, 17963510
    • Barthel D, Hirst J, Blazewicz J, Burke E, Krasnogor N. ProCKSI: A decision support system for protein (structure) comparison, knowledge, similarity and information. BMC Bioinformatics 2007, 8:416. 2222653, 17963510.
    • (2007) BMC Bioinformatics , vol.8 , pp. 416
    • Barthel, D.1    Hirst, J.2    Blazewicz, J.3    Burke, E.4    Krasnogor, N.5
  • 44
    • 67650527109 scopus 로고    scopus 로고
    • Filtering genes for cluster and network analysis
    • 2708160, 19549335
    • Tritchler D, Parkhomenko E, Beyene J. Filtering genes for cluster and network analysis. BMC Bioinformatics 2009, 10:193. 2708160, 19549335.
    • (2009) BMC Bioinformatics , vol.10 , pp. 193
    • Tritchler, D.1    Parkhomenko, E.2    Beyene, J.3
  • 45
    • 0023453329 scopus 로고
    • Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
    • Rousseeuw P. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Mat 1987, 20:53-65.
    • (1987) J Comput Appl Mat , vol.20 , pp. 53-65
    • Rousseeuw, P.1
  • 47
    • 65149084519 scopus 로고    scopus 로고
    • Improving the scalability of rule-based evolutionary learning
    • Bacardit J, Burke E, Krasnogor N. Improving the scalability of rule-based evolutionary learning. Memetic Computing 2009, 1:55-67.
    • (2009) Memetic Computing , vol.1 , pp. 55-67
    • Bacardit, J.1    Burke, E.2    Krasnogor, N.3
  • 48
    • 46949107522 scopus 로고    scopus 로고
    • Data Mining in Proteomics with Learning Classifier Systems
    • Springer, Bull L, Bernado Mansilla E, Holmes J
    • Bacardit J, Stout M, Hirst J, Krasnogor N. Data Mining in Proteomics with Learning Classifier Systems. Learning Classifier Systems in Data Mining 2008, 17-46. Springer, Bull L, Bernado Mansilla E, Holmes J.
    • (2008) Learning Classifier Systems in Data Mining , pp. 17-46
    • Bacardit, J.1    Stout, M.2    Hirst, J.3    Krasnogor, N.4
  • 49
    • 34447331698 scopus 로고    scopus 로고
    • Classification based upon gene expression data: bias and precision of error rates
    • Wood I, Visscher P, Mengersen K. Classification based upon gene expression data: bias and precision of error rates. Bioinformatics 2007, 23(11):1363.
    • (2007) Bioinformatics , vol.23 , Issue.11 , pp. 1363
    • Wood, I.1    Visscher, P.2    Mengersen, K.3
  • 50
    • 25444456388 scopus 로고    scopus 로고
    • Towards precise classification of cancers based on robust gene functional expression profiles
    • 1274255, 15774002
    • Guo Z. Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics 2005, 6:58. 1274255, 15774002.
    • (2005) BMC Bioinformatics , vol.6 , pp. 58
    • Guo, Z.1
  • 52
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • 102409, 10592173
    • Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27. 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27
    • Kanehisa, M.1    Goto, S.2
  • 53
    • 25444502609 scopus 로고    scopus 로고
    • PAGE: parametric analysis of gene set enrichment
    • 1183189, 15941488
    • Kim S, Volsky D. PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005, 6:144. 1183189, 15941488.
    • (2005) BMC Bioinformatics , vol.6 , pp. 144
    • Kim, S.1    Volsky, D.2
  • 54
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B (Methodological) 1995, 57:289-300.
    • (1995) J Roy Statist Soc Ser B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 56
    • 0040596930 scopus 로고    scopus 로고
    • The B cell transcriptional coactivator BOB1/OBF1 gene fuses to the LAZ3/BCL6 gene by t(3;11)(q27;q23.1) chromosomal translocation in a B cell leukemia line (Karpas 231)
    • Galiéque Z, Quief S, Hildebrand M, Denis C, Lecocq G, Collyn-d'Hooghe M, Bastard C, Yuille M, Dyer M, Kerckaert J. The B cell transcriptional coactivator BOB1/OBF1 gene fuses to the LAZ3/BCL6 gene by t(3;11)(q27;q23.1) chromosomal translocation in a B cell leukemia line (Karpas 231). Leukemia 1996, 10(4):579.
    • (1996) Leukemia , vol.10 , Issue.4 , pp. 579
    • Galiéque, Z.1    Quief, S.2    Hildebrand, M.3    Denis, C.4    Lecocq, G.5    Collyn-d'Hooghe, M.6    Bastard, C.7    Yuille, M.8    Dyer, M.9    Kerckaert, J.10


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