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Volumn 31, Issue 13, 2015, Pages 2115-2122

Pattern recognition methods to relate time profiles of gene expression with phenotypic data: A comparative study

Author keywords

[No Author keywords available]

Indexed keywords

ANTIFIBRINOLYTIC AGENT; BENZO[A]PYRENE; MENADIONE;

EID: 84936753964     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv108     Document Type: Article
Times cited : (6)

References (41)
  • 1
    • 77949829999 scopus 로고    scopus 로고
    • In vitro neurotoxicity of PBDE-99: Immediate and concentration-dependent effects on protein expression in cerebral cortex cells
    • Alm,H. et al. (2009) In vitro neurotoxicity of PBDE-99: immediate and concentration-dependent effects on protein expression in cerebral cortex cells. J. Proteome Res., 9, 1226-1235.
    • (2009) J. Proteome Res. , vol.9 , pp. 1226-1235
    • Alm, H.1
  • 2
    • 8844277626 scopus 로고    scopus 로고
    • Analyzing time series gene expression data
    • Bar-Joseph,Z. (2004) Analyzing time series gene expression data. Bioinformatics, 20, 2493-2503.
    • (2004) Bioinformatics , vol.20 , pp. 2493-2503
    • Bar-Joseph, Z.1
  • 3
    • 84863887694 scopus 로고    scopus 로고
    • Studying and modelling dynamic biological processes using time-series gene expression data
    • Bar-Joseph,Z. et al. (2012) Studying and modelling dynamic biological processes using time-series gene expression data. Nat. Rev. Genet., 13, 552-564.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 552-564
    • Bar-Joseph, Z.1
  • 4
    • 34249651218 scopus 로고    scopus 로고
    • Benzo[a]pyrene-dependent activation of transcription factors NF-kappaB and AP-1 related to tumor promotion in hepatoma cell cultures
    • Bolotina,N.A. et al. (2007) Benzo[a]pyrene-dependent activation of transcription factors NF-kappaB and AP-1 related to tumor promotion in hepatoma cell cultures. Biochemistry, 72, 552-557.
    • (2007) Biochemistry , vol.72 , pp. 552-557
    • Bolotina, N.A.1
  • 5
    • 0036085639 scopus 로고    scopus 로고
    • Cancer risk assessment, indicators, and guidelines for polycyclic aromatic hydrocarbons in the ambient air
    • Bostrom,C.E. et al. (2002) Cancer risk assessment, indicators, and guidelines for polycyclic aromatic hydrocarbons in the ambient air. Environ. Health Perspect., 110, 451-488.
    • (2002) Environ. Health Perspect. , vol.110 , pp. 451-488
    • Bostrom, C.E.1
  • 6
    • 77951529058 scopus 로고    scopus 로고
    • Global gene expression analysis reveals differences in cellular responses to hydroxyl-and superoxide anion radical-induced oxidative stress in caco-2 cells
    • Briede,J.J. et al. (2010) Global gene expression analysis reveals differences in cellular responses to hydroxyl-and superoxide anion radical-induced oxidative stress in caco-2 cells. Toxicol. Sci., 114, 193-203.
    • (2010) Toxicol. Sci. , vol.114 , pp. 193-203
    • Briede, J.J.1
  • 7
    • 84882584643 scopus 로고    scopus 로고
    • DTW4Omics: Comparing patterns in biological time series
    • Cavill,R. et al. (2013) DTW4Omics: comparing patterns in biological time series. PLoS one, 8, e71823.
    • (2013) PLoS One , vol.8 , pp. e71823
    • Cavill, R.1
  • 9
    • 26844458204 scopus 로고    scopus 로고
    • Mixture of linear mixed models for clustering gene expression profiles from repeated microarray experiments
    • Celeux,G. et al. (2005) Mixture of linear mixed models for clustering gene expression profiles from repeated microarray experiments. Stat. Model., 5, 243-267.
    • (2005) Stat. Model. , vol.5 , pp. 243-267
    • Celeux, G.1
  • 10
    • 84876467333 scopus 로고    scopus 로고
    • The comparative toxicogenomics database: Update 2013
    • Davis,A.P. et al. (2013) The comparative toxicogenomics database: update 2013. Nucleic Acids Res., 41, D1104-D1114.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D1104-D1114
    • Davis, A.P.1
  • 11
    • 84890460044 scopus 로고    scopus 로고
    • Pattern recognition in bioinformatics
    • de Ridder,D. et al. (2013) Pattern recognition in bioinformatics. Brief Bioinform., 14, 633-647.
    • (2013) Brief Bioinform. , vol.14 , pp. 633-647
    • De Ridder, D.1
  • 12
    • 84874385559 scopus 로고    scopus 로고
    • Time series analysis of oxidative stress response patterns in HepG2: A toxicogenomics approach
    • Deferme,L. et al. (2013) Time series analysis of oxidative stress response patterns in HepG2: A toxicogenomics approach. Toxicology, 306, 24-34.
    • (2013) Toxicology , vol.306 , pp. 24-34
    • Deferme, L.1
  • 13
    • 84891944062 scopus 로고    scopus 로고
    • Analysis of time-resolved gene expression measurements across individuals
    • Elo,L.L. and Schwikowski,B. (2013) Analysis of time-resolved gene expression measurements across individuals. PLoS one, 8, e82340.
    • (2013) PLoS One , vol.8 , pp. e82340
    • Elo, L.L.1    Schwikowski, B.2
  • 14
    • 33646344978 scopus 로고    scopus 로고
    • STEM: A tool for the analysis of short time series gene expression data
    • Ernst,J. and Bar-Joseph,Z. (2006) STEM: A tool for the analysis of short time series gene expression data. BMC bioinformatics, 7, 191.
    • (2006) BMC Bioinformatics , vol.7 , pp. 191
    • Ernst, J.1    Bar-Joseph, Z.2
  • 15
    • 28644452470 scopus 로고    scopus 로고
    • Clustering short time series gene expression data
    • Ernst,J. et al. (2005) Clustering short time series gene expression data. Bioinformatics, 21(Suppl. 1), i159-i168.
    • (2005) Bioinformatics , vol.21 , pp. i159-i168
    • Ernst, J.1
  • 16
    • 40949085272 scopus 로고    scopus 로고
    • Pathway analysis tools and toxicogenomics reference databases for risk assessment
    • Ganter,B. et al. (2008) Pathway analysis tools and toxicogenomics reference databases for risk assessment. Pharmacogenomics, 9, 35-54.
    • (2008) Pharmacogenomics , vol.9 , pp. 35-54
    • Ganter, B.1
  • 17
    • 70349448250 scopus 로고    scopus 로고
    • Computing and visualizing dynamic time warping alignments in R: The dtw package
    • Giorgino,T. (2009) Computing and visualizing dynamic time warping alignments in R: The dtw package. J. Stat. Softw., 31, 1-24.
    • (2009) J. Stat. Softw. , vol.31 , pp. 1-24
    • Giorgino, T.1
  • 18
    • 54949126376 scopus 로고    scopus 로고
    • FlexMix version 2: Finite mixtures with concomitant variables and varying and constant parameters
    • Grün,B. and Leisch,F. (2008) FlexMix version 2: finite mixtures with concomitant variables and varying and constant parameters. J. Stat. Softw., 28, 1-35.
    • (2008) J. Stat. Softw. , vol.28 , pp. 1-35
    • Grün, B.1    Leisch, F.2
  • 19
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan,D. and Weinberg,R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70.
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 20
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of cancer: The next generation
    • Hanahan,D. and Weinberg,R.A. (2011) Hallmarks of cancer: The next generation. Cell, 144, 646-674.
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 21
    • 84875900573 scopus 로고    scopus 로고
    • Performance in omics analyses of blood samples in long-term storage: Opportunities for the exploitation of existing biobanks in environmental health research
    • Hebels,D.G. et al. (2013) Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research. Environ. Health Perspect, 121, 480-487.
    • (2013) Environ. Health Perspect , vol.121 , pp. 480-487
    • Hebels, D.G.1
  • 22
    • 84876008750 scopus 로고    scopus 로고
    • The ConsensusPathDB interaction database: 2013 update
    • Kamburov,A. et al. (2013) The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res., 41, D793-D800.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D793-D800
    • Kamburov, A.1
  • 23
    • 0009660144 scopus 로고
    • Heuristic approaches to spatial analysis in archaeology
    • Kintigh,K.W. and Ammerman,A.J. (1982) Heuristic approaches to spatial analysis in archaeology. Am. Antiq., 47, 31-63.
    • (1982) Am. Antiq. , vol.47 , pp. 31-63
    • Kintigh, K.W.1    Ammerman, A.J.2
  • 24
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Langfelder,P. and Horvath,F. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, F.2
  • 25
    • 11244333649 scopus 로고    scopus 로고
    • FlexMix: A general framework for finite mixture models and latent class regression in R
    • Leisch,F. (2004) FlexMix: A general framework for finite mixture models and latent class regression in R. J. Stat. Softw., 11, 1-18.
    • (2004) J. Stat. Softw. , vol.11 , pp. 1-18
    • Leisch, F.1
  • 26
    • 24044470614 scopus 로고    scopus 로고
    • Clustering of time series data-A survey
    • Liao,T.W. (2005) Clustering of time series data-A survey. Pattern Recogn., 38, 1857-1874.
    • (2005) Pattern Recogn. , vol.38 , pp. 1857-1874
    • Liao, T.W.1
  • 27
    • 0036260697 scopus 로고    scopus 로고
    • Cellular response to oxidative stress: Signaling for suicide and survival
    • Martindale,J.L. and Holbrook,N.J. (2002) Cellular response to oxidative stress: signaling for suicide and survival. J. Cell Physiol., 192, 1-15.
    • (2002) J. Cell Physiol. , vol.192 , pp. 1-15
    • Martindale, J.L.1    Holbrook, N.J.2
  • 28
    • 2942694772 scopus 로고    scopus 로고
    • Artificial gene networks for objective comparison of analysis algorithms
    • Mendes,P. et al. (2003) Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics, 19(Suppl. 2), ii122-ii129.
    • (2003) Bioinformatics , vol.19 , pp. ii122-ii129
    • Mendes, P.1
  • 29
    • 0041875229 scopus 로고    scopus 로고
    • On spectral clustering: Analysis and an algorithm
    • MIT Press, Cambridge, MA
    • Ng,A.Y. et al. (2001) On spectral clustering: analysis and an algorithm. In: Proceedings of Advances in Neural Information Processing Systems, Vol. 14, MIT Press, Cambridge, MA, pp. 849-856.
    • (2001) Proceedings of Advances in Neural Information Processing Systems , vol.14 , pp. 849-856
    • Ng, A.Y.1
  • 30
    • 33749117778 scopus 로고    scopus 로고
    • Simulation of microarray data with realistic characteristics
    • Nykter,M. et al. (2006) Simulation of microarray data with realistic characteristics. BMC Bioinformatics, 7, 349.
    • (2006) BMC Bioinformatics , vol.7 , pp. 349
    • Nykter, M.1
  • 31
    • 33747872953 scopus 로고    scopus 로고
    • Phenotypic anchoring of acetominophen-induced oxidative stress with gene expression profiles in rat liver
    • Powell,C.L. et al. (2006) Phenotypic anchoring of acetominophen-induced oxidative stress with gene expression profiles in rat liver. Toxicol. Sci., 93, 213-222.
    • (2006) Toxicol. Sci. , vol.93 , pp. 213-222
    • Powell, C.L.1
  • 32
    • 84926507971 scopus 로고    scopus 로고
    • Limma powers differential expression analysis for RNA-sequencing and microarray studies
    • Epub ahead of print
    • Ritchie,M.E. et al. (2015) Limma powers differential expression analysis for RNA-sequencing and microarray studies. Nucleic Acids Res., [Epub ahead of print, doi:10.1093/nar/gkv007].
    • (2015) Nucleic Acids Res.
    • Ritchie, M.E.1
  • 33
    • 77949514786 scopus 로고    scopus 로고
    • Mixtures of regression models for time course gene expression data: Evaluation of initialization and random effects
    • Scharl,T. et al. (2010) Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects. Bioinformatics, 26, 370-377.
    • (2010) Bioinformatics , vol.26 , pp. 370-377
    • Scharl, T.1
  • 34
    • 66349094090 scopus 로고    scopus 로고
    • Clustered alignments of gene-expression time series data
    • Smith,A.A. et al. (2009) Clustered alignments of gene-expression time series data. Bioinformatics, 25, i119-i127.
    • (2009) Bioinformatics , vol.25 , pp. i119-i127
    • Smith, A.A.1
  • 35
    • 24944539029 scopus 로고    scopus 로고
    • Consensus clustering and functional interpretation of geneexpression data
    • Swift, et al. (2004) Consensus clustering and functional interpretation of geneexpression data. Genome Biol., 5, R94.
    • (2004) Genome Biol. , vol.5 , pp. R94
    • Swift1
  • 36
    • 30344486684 scopus 로고    scopus 로고
    • Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium
    • Tan,Y. et al. (2006) Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. Bioinformatics, 22, 77-87.
    • (2006) Bioinformatics , vol.22 , pp. 77-87
    • Tan, Y.1
  • 38
    • 77956919845 scopus 로고    scopus 로고
    • Time series analysis of benzo[A]pyrene-induced transcriptome changes suggests that a network of transcription factors regulates the effects on functional gene sets
    • van Delft,J.H. et al. (2010) Time series analysis of benzo[A]pyrene-induced transcriptome changes suggests that a network of transcription factors regulates the effects on functional gene sets. Toxicol. Sci., 117, 381-392.
    • (2010) Toxicol. Sci. , vol.117 , pp. 381-392
    • Van Delft, J.H.1
  • 39
    • 84872568885 scopus 로고    scopus 로고
    • Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
    • Xia,L.C. et al. (2013) Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics, 29, 230-237.
    • (2013) Bioinformatics , vol.29 , pp. 230-237
    • Xia, L.C.1
  • 40
    • 11244352554 scopus 로고    scopus 로고
    • Kernlab-an S4 package for kernel methods in R
    • Zeileis,A. et al. (2004) Kernlab-an S4 package for kernel methods in R. J. Stat. Softw., 11, 1-20.
    • (2004) J. Stat. Softw. , vol.11 , pp. 1-20
    • Zeileis, A.1
  • 41
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene coexpression network analysis
    • Zhang,B. and Horvath,S. (2005) A general framework for weighted gene coexpression network analysis. Stat. Appl. Genet. Mol., 4, 1.
    • (2005) Stat. Appl. Genet. Mol. , vol.4 , pp. 1
    • Zhang, B.1    Horvath, S.2


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