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Volumn 6, Issue , 2012, Pages

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

Author keywords

Feature selection; Gene expression data; Gene Regulatory Network inference; LARS; Stability selection

Indexed keywords

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 84869882656     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-145     Document Type: Article
Times cited : (340)

References (38)
  • 1
    • 0030848624 scopus 로고    scopus 로고
    • A test case of correlation metric construction of a reaction pathway from measurements
    • Arkin A, Shen P, Ross J. A test case of correlation metric construction of a reaction pathway from measurements. Science 1997, 277(5330):1275-1279. [http://www.sciencemag.org/cgi/reprint/277/5330/1275.pdf].
    • (1997) Science , vol.277 , Issue.5330 , pp. 1275-1279
    • Arkin, A.1    Shen, P.2    Ross, J.3
  • 2
    • 0031616241 scopus 로고    scopus 로고
    • REVEAL, a general reverse engineering algorithm for inference of genetic network architectures
    • Liang S, Fuhrman S, Somogyi R. REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998, 3:18-29.
    • (1998) Pac Symp Biocomput , vol.3 , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 3
    • 0032611513 scopus 로고    scopus 로고
    • Modeling gene expression with differential equations
    • Chen T, He HL, Church GM. Modeling gene expression with differential equations. Pac Symp Biocomput 1999, 4:29-40.
    • (1999) Pac Symp Biocomput , vol.4 , pp. 29-40
    • Chen, T.1    He, H.L.2    Church, G.M.3
  • 4
    • 0033677274 scopus 로고    scopus 로고
    • Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function
    • 10.1089/106652700750050817, 11108466
    • Akutsu T, Miyano S, Kuhara S. Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. J Comput Biol 2000, 7(3-4):331-343. 10.1089/106652700750050817, 11108466.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 331-343
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 5
    • 0037197936 scopus 로고    scopus 로고
    • Reverse engineering gene networks using singular value decomposition and robust regression
    • 10.1073/pnas.092576199, 122920, 11983907
    • Yeung MKS, Tegnér J, Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci USA 2002, 99(9):6163-6168. [http://www.pnas.org/content/99/9/6163.abstract], 10.1073/pnas.092576199, 122920, 11983907.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.9 , pp. 6163-6168
    • Yeung, M.K.S.1    Tegnér, J.2    Collins, J.J.3
  • 6
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling
    • 10.1073/pnas.0933416100, 156306, 12730377
    • Tegner J, Yeung MKS, Hasty J, Collins JJ. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci USA 2003, 100(10):5944-5949. 10.1073/pnas.0933416100, 156306, 12730377.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.10 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.K.S.2    Hasty, J.3    Collins, J.J.4
  • 7
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • 10.1126/science.1081900, 12843395
    • Gardner TS, Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301(5629):102-105. 10.1126/science.1081900, 12843395.
    • (2003) Science , vol.301 , Issue.5629 , pp. 102-105
    • Gardner, T.S.1    Bernardo, D.2    Lorenz, D.3    Collins, J.J.4
  • 8
    • 20844452570 scopus 로고    scopus 로고
    • A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
    • 10.1093/bioinformatics/bti415, 15802287
    • Chen KC, Wang TY, Tseng HH, Huang CYF, Kao CY. A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics 2005, 21(12):2883-2890. 10.1093/bioinformatics/bti415, 15802287.
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2883-2890
    • Chen, K.C.1    Wang, T.Y.2    Tseng, H.H.3    Huang, C.Y.F.4    Kao, C.Y.5
  • 10
    • 33645307955 scopus 로고    scopus 로고
    • Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
    • 10.1093/bioinformatics/btl003, 16418235
    • Bansal M, Della G, Bernardo D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 2006, 22(7):815-822. 10.1093/bioinformatics/btl003, 16418235.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 815-822
    • Bansal, M.1    Della, G.2    Bernardo, D.3
  • 11
    • 77952663448 scopus 로고    scopus 로고
    • TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
    • 10.1186/1471-2105-11-154, 2862045, 20338053
    • Zoppoli P, Morganella S, Ceccarelli M. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 2010, 11:154. 10.1186/1471-2105-11-154, 2862045, 20338053.
    • (2010) BMC Bioinformatics , vol.11 , pp. 154
    • Zoppoli, P.1    Morganella, S.2    Ceccarelli, M.3
  • 12
    • 0034710924 scopus 로고    scopus 로고
    • Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
    • 10.1073/pnas.220392197, 17315, 11027309
    • Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci USA 2000, 97(22):12182-12186. 10.1073/pnas.220392197, 17315, 11027309.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.22 , pp. 12182-12186
    • Butte, A.J.1    Tamayo, P.2    Slonim, D.3    Golub, T.R.4    Kohane, I.S.5
  • 13
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular contexts
    • 10.1186/1471-2105-7-S1-S7, 1810318, 16723010
    • Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular contexts. BMC Bioinformatics 2006, 7 Suppl 1:S7. 10.1186/1471-2105-7-S1-S7, 1810318, 16723010.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 1
    • Margolin, A.A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5    Dalla Favera, R.6    Califano, A.7
  • 14
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • 10.1371/journal.pbio.0050008, 1764438, 17214507
    • Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5:e8. 10.1371/journal.pbio.0050008, 1764438, 17214507.
    • (2007) PLoS Biol , vol.5
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6    Kasif, S.7    Collins, J.J.8    Gardner, T.S.9
  • 15
    • 15944367731 scopus 로고    scopus 로고
    • Reconstructing biological networks using conditional correlation analysis
    • 10.1093/bioinformatics/bti064, 15486043
    • Rice J, Tu Y, Stolovitzky G. Reconstructing biological networks using conditional correlation analysis. Bioinformatics 2005, 21(6):765-773. 10.1093/bioinformatics/bti064, 15486043.
    • (2005) Bioinformatics , vol.21 , Issue.6 , pp. 765-773
    • Rice, J.1    Tu, Y.2    Stolovitzky, G.3
  • 16
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • 10.1089/106652700750050961, 11108481
    • Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol 2000, 7(3-4):601-620. 10.1089/106652700750050961, 11108481.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'er, D.4
  • 17
    • 0035221560 scopus 로고    scopus 로고
    • Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
    • World Scientific, Altman RB, Dunker AK, Hunter L, Lauerdale K, Klein TE,
    • Hartemink A, Gifford D, Jaakkola T, Young R. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Proceedings of the Pacific Symposium on Biocomputing 2002 2002, 422-433. World Scientific, Altman RB, Dunker AK, Hunter L, Lauerdale K, Klein TE, [http://helix-web.stanford.edu/psb01/abstracts/p422.html].
    • (2002) Proceedings of the Pacific Symposium on Biocomputing 2002 , pp. 422-433
    • Hartemink, A.1    Gifford, D.2    Jaakkola, T.3    Young, R.4
  • 18
    • 4143058645 scopus 로고    scopus 로고
    • Gene networks inference using dynamic Bayesian networks
    • 10.1093/bioinformatics/btg1071, 14534183
    • Perrin B, Ralaivola L, Mazurie A, Bottani S, Mallet J, d'Alche Buc F. Gene networks inference using dynamic Bayesian networks. Bioinformatics 2003, 19(suppl 2):ii138-ii148. 10.1093/bioinformatics/btg1071, 14534183.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Perrin, B.1    Ralaivola, L.2    Mazurie, A.3    Bottani, S.4    Mallet, J.5    d'Alche Buc, F.6
  • 19
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • 10.1126/science.1094068, 14764868
    • Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303(5659):799. 10.1126/science.1094068, 14764868.
    • (2004) Science , vol.303 , Issue.5659 , pp. 799
    • Friedman, N.1
  • 20
    • 77958570788 scopus 로고    scopus 로고
    • Inferring regulatory networks from expression data using tree-based methods
    • 10.1371/journal.pone.0012776, 2946910, 20927193
    • Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P. Inferring regulatory networks from expression data using tree-based methods. PLoS One 2010, 5(9):e12776. 10.1371/journal.pone.0012776, 2946910, 20927193.
    • (2010) PLoS One , vol.5 , Issue.9
    • Huynh-Thu, V.A.1    Irrthum, A.2    Wehenkel, L.3    Geurts, P.4
  • 21
    • 38449088751 scopus 로고    scopus 로고
    • Inferring cellular networks - a review
    • 10.1186/1471-2105-8-S6-S5, 2230506, 18269699
    • Markowetz F, Spang R. Inferring cellular networks - a review. BMC Bioinformatics 2007, 8(Suppl 6):S5. [http://www.biomedcentral.com/1471-2105/8/S6/S5], 10.1186/1471-2105-8-S6-S5, 2230506, 18269699.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 6
    • Markowetz, F.1    Spang, R.2
  • 22
    • 77950910419 scopus 로고    scopus 로고
    • Revealing strengths and weaknesses of methods for gene network inference
    • 10.1073/pnas.0913357107, 2851985, 20308593
    • Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G. Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci USA 2010, 107(14):6286-6291. http://www.pnas.org/content/107/14/6286.abstract, 10.1073/pnas.0913357107, 2851985, 20308593.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.14 , pp. 6286-6291
    • Marbach, D.1    Prill, R.J.2    Schaffter, T.3    Mattiussi, C.4    Floreano, D.5    Stolovitzky, G.6
  • 23
    • 33747163541 scopus 로고    scopus 로고
    • High dimensional graphs and variable selection with the Lasso
    • Meinshausen N, Bühlmann P. High dimensional graphs and variable selection with the Lasso. Ann Stat 2006, 34:1436-1462.
    • (2006) Ann Stat , vol.34 , pp. 1436-1462
    • Meinshausen, N.1    Bühlmann, P.2
  • 27
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B 1996, 58:267-288.
    • (1996) J R Stat Soc Ser B , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 29
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn 2001, 45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 32
    • 76749107542 scopus 로고    scopus 로고
    • Online Learning for Matrix Factorization and Sparse Coding
    • Mairal J, Bach F, Ponce J, Sapiro G. Online Learning for Matrix Factorization and Sparse Coding. J Mach Learn Res 2010, 11:19-60. [http://jmlr.csail.mit.edu/papers/v11/mairal10a.html].
    • (2010) J Mach Learn Res , vol.11 , pp. 19-60
    • Mairal, J.1    Bach, F.2    Ponce, J.3    Sapiro, G.4
  • 33
    • 79961200389 scopus 로고    scopus 로고
    • GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods
    • 10.1093/bioinformatics/btr373, 21697125
    • Schaffter T, Marbach D, Floreano D. GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics 2011, 27(16):2263-2270. [http://bioinformatics.oxfordjournals.org/content/27/16/2263.abstract], 10.1093/bioinformatics/btr373, 21697125.
    • (2011) Bioinformatics , vol.27 , Issue.16 , pp. 2263-2270
    • Schaffter, T.1    Marbach, D.2    Floreano, D.3
  • 34
    • 59649110273 scopus 로고    scopus 로고
    • Generating realistic in silico gene networks for performance assessment of reverse engineering methods
    • 10.1089/cmb.2008.09TT, 19183003
    • Marbach D, Schaffter T, Mattiussi C, Floreano D. Generating realistic in silico gene networks for performance assessment of reverse engineering methods. J Comput Biol 2009, 16(2):229-239. [http://online.liebertpub.com/doi/abs/10.1089/cmb.2008.09TT], 10.1089/cmb.2008.09TT, 19183003.
    • (2009) J Comput Biol , vol.16 , Issue.2 , pp. 229-239
    • Marbach, D.1    Schaffter, T.2    Mattiussi, C.3    Floreano, D.4
  • 35
    • 38549134505 scopus 로고    scopus 로고
    • Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
    • 10.1093/nar/gkm815, 2238822, 17932051
    • Faith J, Driscoll M, Fusaro V, Cosgrove E, Hayete B, Juhn F, Schneider S, Gardner T. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 2008, 36(Database issue):D866-D870. 10.1093/nar/gkm815, 2238822, 17932051.
    • (2008) Nucleic Acids Res , vol.36 , Issue.DATABASE ISSUE
    • Faith, J.1    Driscoll, M.2    Fusaro, V.3    Cosgrove, E.4    Hayete, B.5    Juhn, F.6    Schneider, S.7    Gardner, T.8
  • 37
    • 84861168271 scopus 로고    scopus 로고
    • Inferring gene regulatory networks by ANOVA
    • 10.1093/bioinformatics/bts143, 22467911
    • Küffner R, Petri T, Tavakkolkhah P, Windhager L, Zimmer R. Inferring gene regulatory networks by ANOVA. Bioinformatics 2012, 28(10):1376-1382. 10.1093/bioinformatics/bts143, 22467911.
    • (2012) Bioinformatics , vol.28 , Issue.10 , pp. 1376-1382
    • Küffner, R.1    Petri, T.2    Tavakkolkhah, P.3    Windhager, L.4    Zimmer, R.5
  • 38
    • 49549104230 scopus 로고    scopus 로고
    • SIRENE: Supervised inference of regulatory networks
    • 10.1093/bioinformatics/btn273, 18689844
    • Mordelet F, Vert JP. SIRENE: Supervised inference of regulatory networks. Bioinformatics 2008, 24(16):i76-i82. 10.1093/bioinformatics/btn273, 18689844.
    • (2008) Bioinformatics , vol.24 , Issue.16
    • Mordelet, F.1    Vert, J.P.2


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