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Volumn 7, Issue 3, 2012, Pages

Bagging statistical network inference from large-scale gene expression data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAGGING STATISTICAL NETWORK INFERENCE; BAYES THEOREM; BOOTSTRAPPING; CONTROLLED STUDY; FUZZY SYSTEM; GENE EXPRESSION; GENE REGULATORY NETWORK; MICROARRAY ANALYSIS; NONHUMAN; PROTEIN ASSEMBLY; PROTEIN PROTEIN INTERACTION; RANDOMIZATION; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; TRANSCRIPTION REGULATION;

EID: 84859125037     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033624     Document Type: Article
Times cited : (102)

References (63)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási AL, Oltvai ZN, (2004) Network biology: Understanding the cell's functional organization. Nature Reviews 5: 101-113.
    • (2004) Nature Reviews , vol.5 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.N.2
  • 2
    • 79958145357 scopus 로고    scopus 로고
    • Network Biology: A direct approach to study biological function
    • Emmert-Streib F, Glazko G, (2011) Network Biology: A direct approach to study biological function. Wiley Interdiscip Rev Syst Biol Med 3: 379-391.
    • (2011) Wiley Interdiscip Rev Syst Biol Med , vol.3 , pp. 379-391
    • Emmert-Streib, F.1    Glazko, G.2
  • 3
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman S, (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 22: 437-467.
    • (1969) Journal of Theoretical Biology , vol.22 , pp. 437-467
    • Kauffman, S.1
  • 4
    • 33751361595 scopus 로고    scopus 로고
    • Cambridge; New York, Cambridge University Press
    • Palsson B, (2006) Systems Biology Cambridge; New York Cambridge University Press.
    • (2006) Systems Biology
    • Palsson, B.1
  • 5
    • 71349087490 scopus 로고    scopus 로고
    • A unifying view of 21st century systems biology
    • Vidal M, (2009) A unifying view of 21st century systems biology. FEBS Letters 583: 3891-3894.
    • (2009) FEBS Letters , vol.583 , pp. 3891-3894
    • Vidal, M.1
  • 6
    • 0004078878 scopus 로고
    • The strategy of the genes
    • Geo, Allen & Unwin, London
    • Waddington C, (1957) The strategy of the genes. Geo, Allen & Unwin, London.
    • (1957)
    • Waddington, C.1
  • 7
    • 70249114542 scopus 로고    scopus 로고
    • Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference
    • Wiley-Blackwell
    • Stolovitzky G, Califano A, eds. (2007) Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference. Wiley-Blackwell.
    • (2007)
    • Stolovitzky, G.1    Califano, A.2
  • 9
    • 77957141016 scopus 로고    scopus 로고
    • Inferring the conservative causal core of gene regulatory networks
    • Altay G, Emmert-Streib F, (2010) Inferring the conservative causal core of gene regulatory networks. BMC Systems Biology 4: 132.
    • (2010) BMC Systems Biology , vol.4 , pp. 132
    • Altay, G.1    Emmert-Streib, F.2
  • 10
    • 20744440332 scopus 로고    scopus 로고
    • Inferring genetic regulatory logic from expression data
    • Bulashevska S, Eils R, (2005) Inferring genetic regulatory logic from expression data. Bioinformatics 21: 2706-2713.
    • (2005) Bioinformatics , vol.21 , pp. 2706-2713
    • Bulashevska, S.1    Eils, R.2
  • 11
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith J, Hayete B, Thaden J, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: e8.
    • (2007) PLoS Biol , vol.5
    • Faith, J.1    Hayete, B.2    Thaden, J.3    Mogno, I.4    Wierzbowski, J.5
  • 12
    • 12344321571 scopus 로고    scopus 로고
    • Discovery of meaningful associations in genomic data using partial correlation coefficients
    • de la Fuente A, Bing N, Hoeschele I, Mendes P, (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20: 3565-3574.
    • (2004) Bioinformatics , vol.20 , pp. 3565-3574
    • de la Fuente, A.1    Bing, N.2    Hoeschele, I.3    Mendes, P.4
  • 13
    • 68349161006 scopus 로고    scopus 로고
    • Reverse engineering of gene regulatory networks: A comparative study
    • Hache H, Lehrach H, Herwig R, (2009) Reverse engineering of gene regulatory networks: A comparative study. EURASIP J Bioinform Syst Biol 2009: 617281.
    • (2009) EURASIP J Bioinform Syst Biol , vol.2009 , pp. 617281
    • Hache, H.1    Lehrach, H.2    Herwig, R.3
  • 14
    • 58149349958 scopus 로고    scopus 로고
    • Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
    • Luo W, Hankenson K, Woolf P, (2008) Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics 9: 467.
    • (2008) BMC Bioinformatics , vol.9 , pp. 467
    • Luo, W.1    Hankenson, K.2    Woolf, P.3
  • 16
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky, et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7: S7.
    • (2006) BMC Bioinformatics , vol.7
    • Margolin, A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky5
  • 18
    • 33749825955 scopus 로고    scopus 로고
    • Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
    • Werhli A, Grzegorczyk M, Husmeier D, (2006) Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 22: 2523-31.
    • (2006) Bioinformatics , vol.22 , pp. 2523-2531
    • Werhli, A.1    Grzegorczyk, M.2    Husmeier, D.3
  • 19
    • 27744474082 scopus 로고    scopus 로고
    • A causal inference approach for constructing transcriptional regulatory networks
    • Xing B, van der Laan M, (2005) A causal inference approach for constructing transcriptional regulatory networks. Bioinformatics 21: 4007-4013.
    • (2005) Bioinformatics , vol.21 , pp. 4007-4013
    • Xing, B.1    van der Laan, M.2
  • 20
    • 34547146985 scopus 로고    scopus 로고
    • Network Medicine - From Obesity to the Diseasome
    • Barabási AL, (2007) Network Medicine - From Obesity to the "Diseasome". N Engl J Med 357: 404-407.
    • (2007) N Engl J Med , vol.357 , pp. 404-407
    • Barabási, A.L.1
  • 22
    • 67349276056 scopus 로고    scopus 로고
    • A network medicine approach to human disease
    • Zanzoni A, Soler-Lopez M, Aloy P, (2009) A network medicine approach to human disease. FEBS Letters 583: 1759-1765.
    • (2009) FEBS Letters , vol.583 , pp. 1759-1765
    • Zanzoni, A.1    Soler-Lopez, M.2    Aloy, P.3
  • 23
    • 77957110013 scopus 로고    scopus 로고
    • Advantages and limitations of current network inference methods
    • De Smet R, Marchal K, (2010) Advantages and limitations of current network inference methods. Nature Reviews Microbiology 8: 717-729.
    • (2010) Nature Reviews Microbiology , vol.8 , pp. 717-729
    • De Smet, R.1    Marchal, K.2
  • 24
    • 84859112389 scopus 로고    scopus 로고
    • Statistical inference and reverse engineering of gene regulatory networks from observational expression data
    • Emmert-Streib F, Glazko G, Altay G, de Matos Simoes R, (2012) Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Frontiers in Genetics 3: 8.
    • (2012) Frontiers in Genetics , vol.3 , pp. 8
    • Emmert-Streib, F.1    Glazko, G.2    Altay, G.3    de Matos Simoes, R.4
  • 26
    • 84859149116 scopus 로고    scopus 로고
    • How to infer gene networks from expression profiles, revisited
    • Penfold CA, Wild DL, (2011) How to infer gene networks from expression profiles, revisited. Interface Focus 1: 857-870.
    • (2011) Interface Focus , vol.1 , pp. 857-870
    • Penfold, C.A.1    Wild, D.L.2
  • 27
    • 0242295767 scopus 로고    scopus 로고
    • Bayesian factor regression models in the "large p, small n" paradigm
    • Oxford University Press
    • West M, (2003) Bayesian factor regression models in the "large p, small n" paradigm. Bayesian Statistics 7 Oxford University Press pp. 723-732.
    • (2003) Bayesian Statistics 7 , pp. 723-732
    • West, M.1
  • 28
    • 0030211964 scopus 로고    scopus 로고
    • Bagging Predictors
    • Breiman L, (1996) Bagging Predictors. Machine Learning 24: 123-140.
    • (1996) Machine Learning , vol.24 , pp. 123-140
    • Breiman, L.1
  • 31
    • 77958570788 scopus 로고    scopus 로고
    • Inferring regulatory networks from expression data using tree-based methods
    • Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P, (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5: e12776.
    • (2010) PLoS ONE , vol.5
    • Huynh-Thu, V.A.1    Irrthum, A.2    Wehenkel, L.3    Geurts, P.4
  • 32
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman L, (2001) Random Forests. Machine Learning 45: 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 34
    • 77953255983 scopus 로고    scopus 로고
    • A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers
    • Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, et al. (2010) A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Molecular Systems Biology 6: 377.
    • (2010) Molecular Systems Biology , vol.6 , pp. 377
    • Lefebvre, C.1    Rajbhandari, P.2    Alvarez, M.J.3    Bandaru, P.4    Lim, W.K.5
  • 35
    • 68349116164 scopus 로고    scopus 로고
    • The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain
    • Zhao X, D Arca D, Lim WK, Brahmachary M, Carro MS, et al. (2009) The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Developmental Cell 17: 210-221.
    • (2009) Developmental Cell , vol.17 , pp. 210-221
    • Zhao, X.1    Arca, D.2    Lim, W.K.3    Brahmachary, M.4    Carro, M.S.5
  • 38
    • 55249117952 scopus 로고    scopus 로고
    • A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion
    • Farcomeni A, (2008) A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion. Stat Methods Med Res 17: 347-88.
    • (2008) Stat Methods Med Res , vol.17 , pp. 347-388
    • Farcomeni, A.1
  • 40
    • 0041530047 scopus 로고    scopus 로고
    • Resampling-based multiple testing for microarray data analysis
    • Ge Y, Dudoit S, Speed T, (2003) Resampling-based multiple testing for microarray data analysis. TEST 12: 1-77.
    • (2003) TEST , vol.12 , pp. 1-77
    • Ge, Y.1    Dudoit, S.2    Speed, T.3
  • 41
    • 77954479475 scopus 로고    scopus 로고
    • Local network-based measures to assess the inferability of different regulatory networks
    • Emmert-Streib F, Altay G, (2010) Local network-based measures to assess the inferability of different regulatory networks. IET Systems Biology 4: 277-288.
    • (2010) IET Systems Biology , vol.4 , pp. 277-288
    • Emmert-Streib, F.1    Altay, G.2
  • 42
    • 0041877169 scopus 로고    scopus 로고
    • Estimation of entropy and mutual information
    • Paninski L, (2003) Estimation of entropy and mutual information. Neural Computation 15: 1191-1253.
    • (2003) Neural Computation , vol.15 , pp. 1191-1253
    • Paninski, L.1
  • 43
    • 27844521293 scopus 로고    scopus 로고
    • A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
    • Schäfer J, Strimmer K, (2005) A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics. Statistical Applications in Genetics and Molecular Biology 4: 32.
    • (2005) Statistical Applications in Genetics and Molecular Biology , vol.4 , pp. 32
    • Schäfer, J.1    Strimmer, K.2
  • 44
    • 0040973114 scopus 로고    scopus 로고
    • Entropy estimation of symbol sequences
    • Schürmann T, Grassberger P, (1996) Entropy estimation of symbol sequences. Chaos 6: 414427.
    • (1996) Chaos , vol.6 , pp. 414427
    • Schürmann, T.1    Grassberger, P.2
  • 45
    • 13244267007 scopus 로고    scopus 로고
    • Estimating mutual information using B-spline functions-an improved similarity measure for analysing gene expression data
    • Daub C, Steuer R, Selbig J, Kloska S, (2004) Estimating mutual information using B-spline functions-an improved similarity measure for analysing gene expression data. BMC Bioinformatics 5: 118.
    • (2004) BMC Bioinformatics , vol.5 , pp. 118
    • Daub, C.1    Steuer, R.2    Selbig, J.3    Kloska, S.4
  • 46
    • 38549134505 scopus 로고    scopus 로고
    • Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
    • Faith J, Driscoll M, Fusaro V, Cosgrove E, Hayete B, et al. (2008) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 36: D866-70.
    • (2008) Nucleic Acids Res , vol.36
    • Faith, J.1    Driscoll, M.2    Fusaro, V.3    Cosgrove, E.4    Hayete, B.5
  • 48
    • 33144486498 scopus 로고    scopus 로고
    • SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
    • Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, et al. (2006) SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics 7: 43.
    • (2006) BMC Bioinformatics , vol.7 , pp. 43
    • van den Bulcke, T.1    Van Leemput, K.2    Naudts, B.3    van Remortel, P.4    Ma, H.5
  • 49
    • 0344464762 scopus 로고    scopus 로고
    • Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic bayesian networks
    • Husmeier D, (2003) Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic bayesian networks. Bioinformatics 19: 2271-82.
    • (2003) Bioinformatics , vol.19 , pp. 2271-2282
    • Husmeier, D.1
  • 50
    • 49449086368 scopus 로고    scopus 로고
    • Survival of the sparsest: robust gene networks are parsimonious
    • Leclerc RD, (2008) Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol 4: 213.
    • (2008) Mol Syst Biol , vol.4 , pp. 213
    • Leclerc, R.D.1
  • 51
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball C, Blake J, Botstein D, Butler, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25-29.
    • (2000) Nature Genetics , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.2    Blake, J.3    Botstein, D.4    Butler5
  • 53
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with proteinprotein interactions
    • Jansen R, Greenbaum D, Gerstein M, (2002) Relating whole-genome expression data with proteinprotein interactions. Genome Res 12: 37-46.
    • (2002) Genome Res , vol.12 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 54
    • 0035445792 scopus 로고    scopus 로고
    • A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae
    • Grigoriev A, (2001) A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 29: 3513-9.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3513-3519
    • Grigoriev, A.1
  • 55
    • 36248989626 scopus 로고    scopus 로고
    • Theory and limitations of genetic network inference from microarray data
    • Margolin A, Califano A, (2007) Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci 1115: 51-72.
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 51-72
    • Margolin, A.1    Califano, A.2
  • 56
    • 79959327654 scopus 로고    scopus 로고
    • Structural Influence of gene networks on their inference: Analysis of C3NET
    • Altay G, Emmert-Streib F, (2011) Structural Influence of gene networks on their inference: Analysis of C3NET. Biology Direct 6: 31.
    • (2011) Biology Direct , vol.6 , pp. 31
    • Altay, G.1    Emmert-Streib, F.2
  • 61
    • 34249862287 scopus 로고    scopus 로고
    • Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process
    • Opgen-Rhein R, Strimmer K, (2007) Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process. BMC Bioinformatics 8: S3.
    • (2007) BMC Bioinformatics , vol.8
    • Opgen-Rhein, R.1    Strimmer, K.2
  • 62
    • 5344244656 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
    • R Development Core Team (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
    • (2008)
  • 63
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi G, Nepusz T, (2006) The igraph software package for complex network research. InterJournal Complex Systems pp. 1695.
    • (2006) InterJournal Complex Systems , pp. 1695
    • Csardi, G.1    Nepusz, T.2


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