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Volumn 4, Issue 4, 2012, Pages 311-325

Reverse-engineering human regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

B LYMPHOCYTE RECEPTOR; CARRIER PROTEINS AND BINDING PROTEINS; CD151 ANTIGEN; CD97 ANTIGEN; COMPLEMENT COMPONENT C1R; DNA; GROWTH FACTOR RECEPTOR BOUND PROTEIN 2; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 32; MATRIX METALLOPROTEINASE 14; MESSENGER RNA; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE 3; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE KINASE 2; PROTEIN HOMER 3; PROTEIN SHC; RAF PROTEIN; RAS PROTEIN; RNA; SMAD3 PROTEIN; SMAD4 PROTEIN; SMALL INTERFERING RNA; SUPPRESSOR OF CYTOKINE SIGNALING 3; TISSUE INHIBITOR OF METALLOPROTEINASE 1; TRANSCRIPTION FACTOR;

EID: 84862564150     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.1159     Document Type: Review
Times cited : (41)

References (100)
  • 1
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303:799-805.
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 2
    • 18144442687 scopus 로고    scopus 로고
    • Inferring subnetworks from perturbed expression profiles
    • SUPPL 1
    • Pe'er D, Regev A, Elidan G, Friedman N. Inferring subnetworks from perturbed expression profiles. Bioinformatics 2001, 17(suppl 1):S215-S224.
    • (2001) Bioinformatics , vol.17
    • Pe'er, D.1    Regev, A.2    Elidan, G.3    Friedman, N.4
  • 4
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 6
    • 0037197936 scopus 로고    scopus 로고
    • Reverse engineering gene networks using singular value decomposition and robust regression
    • Yeung MK, Tegner J, Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A 2002, 99:6163-6168.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 6163-6168
    • Yeung, M.K.1    Tegner, J.2    Collins, J.J.3
  • 8
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression. Nat Genet 2001, 27:167-171.
    • (2001) Nat Genet , vol.27 , pp. 167-171
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 9
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene
    • Yuh CH, Bolouri H, Davidson EH. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 1998, 279: 1896-1902.
    • (1998) Science , vol.279 , pp. 1896-1902
    • Yuh, C.H.1    Bolouri, H.2    Davidson, E.H.3
  • 10
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling
    • Tegner J, Yeung MK, Hasty J, Collins JJ. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A 2003, 100:5944-5949.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.K.2    Hasty, J.3    Collins, J.J.4
  • 12
    • 37549003686 scopus 로고    scopus 로고
    • An interview with Sydney Brenner
    • Friedberg EC. An interview with Sydney Brenner. Nat Rev Mol Cell Biol 2008, 9:8-9.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 8-9
    • Friedberg, E.C.1
  • 14
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • TCGA-Consortium. .
    • TCGA-Consortium. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068.
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 20
    • 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, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, et al. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell 2009, 17:210-221.
    • (2009) Dev Cell , vol.17 , pp. 210-221
    • Zhao, X.1    D'Arca, D.2    Lim, W.K.3    Brahmachary, M.4    Carro, M.S.5    Ludwig, T.6    Cardo, C.C.7    Guillemot, F.8    Aldape, K.9    Califano, A.10
  • 22
    • 74249091032 scopus 로고    scopus 로고
    • Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study
    • Hagg S, Skogsberg J, Lundstrom J, Noori P, Nilsson R, Zhong H, Maleki S, Shang MM, Brinne B, Bradshaw M, et al. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study. PLoS Genet 2009, 5:e1000754.
    • (2009) PLoS Genet , vol.5
    • Hagg, S.1    Skogsberg, J.2    Lundstrom, J.3    Noori, P.4    Nilsson, R.5    Zhong, H.6    Maleki, S.7    Shang, M.M.8    Brinne, B.9    Bradshaw, M.10
  • 24
    • 39149143293 scopus 로고    scopus 로고
    • A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
    • Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 2008, 4:169.
    • (2008) Mol Syst Biol , vol.4 , pp. 169
    • Mani, K.M.1    Lefebvre, C.2    Wang, K.3    Lim, W.K.4    Basso, K.5    Dalla-Favera, R.6    Califano, A.7
  • 27
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker T, Sharan R. Protein networks in disease. Genome Res 2008, 18:644-652.
    • (2008) Genome Res , vol.18 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 35
    • 33745248430 scopus 로고    scopus 로고
    • microRNA target predictions in animals
    • SUPPL
    • Rajewsky N. microRNA target predictions in animals. Nat Genet 2006, 38(suppl):S8-S13.
    • (2006) Nat Genet , vol.38
    • Rajewsky, N.1
  • 36
    • 77649222742 scopus 로고    scopus 로고
    • Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells
    • Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, et al. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood 2010, 115:975-984.
    • (2010) Blood , vol.115 , pp. 975-984
    • Basso, K.1    Saito, M.2    Sumazin, P.3    Margolin, A.A.4    Wang, K.5    Lim, W.K.6    Kitagawa, Y.7    Schneider, C.8    Alvarez, M.J.9    Califano, A.10
  • 38
    • 70350569876 scopus 로고    scopus 로고
    • Comparing different ODE modelling approaches for gene regulatory networks
    • Polynikis A, Hogan SJ, di Bernardo M. Comparing different ODE modelling approaches for gene regulatory networks. J Theor Biol 2009, 261:511-530.
    • (2009) J Theor Biol , vol.261 , pp. 511-530
    • Polynikis, A.1    Hogan, S.J.2    di Bernardo, M.3
  • 40
    • 35948963320 scopus 로고    scopus 로고
    • Mathematical models for excitable systems in biology and medicine
    • Ballaro B, Reas PG, Riccardi R. Mathematical models for excitable systems in biology and medicine. Riv Biol 2007, 100:247-266.
    • (2007) Riv Biol , vol.100 , pp. 247-266
    • Ballaro, B.1    Reas, P.G.2    Riccardi, R.3
  • 42
    • 34249950625 scopus 로고    scopus 로고
    • Stochastic simulation of chemical kinetics
    • Gillespie DT. Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 2007, 58:35-55.
    • (2007) Annu Rev Phys Chem , vol.58 , pp. 35-55
    • Gillespie, D.T.1
  • 46
    • 58149213801 scopus 로고    scopus 로고
    • Non-Smad pathways in TGF-beta signaling
    • Zhang YE. Non-Smad pathways in TGF-beta signaling. Cell Res 2009, 19:128-139.
    • (2009) Cell Res , vol.19 , pp. 128-139
    • Zhang, Y.E.1
  • 47
    • 65949099120 scopus 로고    scopus 로고
    • Genetic risk prediction-are we there yet?
    • Kraft P, Hunter DJ. Genetic risk prediction-are we there yet? N Engl J Med 2009, 360:1701-1703.
    • (2009) N Engl J Med , vol.360 , pp. 1701-1703
    • Kraft, P.1    Hunter, D.J.2
  • 48
    • 65949104586 scopus 로고    scopus 로고
    • Genomewide association studies and human disease
    • Hardy J, Singleton A. Genomewide association studies and human disease. N Engl J Med 2009, 360:1759-1768.
    • (2009) N Engl J Med , vol.360 , pp. 1759-1768
    • Hardy, J.1    Singleton, A.2
  • 49
    • 65949107547 scopus 로고    scopus 로고
    • Common genetic variation and human traits
    • Goldstein DB. Common genetic variation and human traits. N Engl J Med 2009, 360:1696-1698.
    • (2009) N Engl J Med , vol.360 , pp. 1696-1698
    • Goldstein, D.B.1
  • 52
    • 55449120805 scopus 로고    scopus 로고
    • Genetic mapping in human disease
    • Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science 2008, 322:881-888.
    • (2008) Science , vol.322 , pp. 881-888
    • Altshuler, D.1    Daly, M.J.2    Lander, E.S.3
  • 53
    • 62549085618 scopus 로고    scopus 로고
    • Human genetic variation and its contribution to complex traits
    • Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet 2009, 10:241-251.
    • (2009) Nat Rev Genet , vol.10 , pp. 241-251
    • Frazer, K.A.1    Murray, S.S.2    Schork, N.J.3    Topol, E.J.4
  • 55
    • 77950339092 scopus 로고    scopus 로고
    • Integrating pathway analysis and genetics of gene expression for genome-wide association studies
    • Zhong H, Yang X, Kaplan LM, Molony C, Schadt EE. Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am J Hum Genet 2010, 86:581-591.
    • (2010) Am J Hum Genet , vol.86 , pp. 581-591
    • Zhong, H.1    Yang, X.2    Kaplan, L.M.3    Molony, C.4    Schadt, E.E.5
  • 58
    • 78650562728 scopus 로고    scopus 로고
    • dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks
    • Jia P, Zheng S, Long J, Zheng W, Zhao Z. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 2011, 27:95-102.
    • (2011) Bioinformatics , vol.27 , pp. 95-102
    • Jia, P.1    Zheng, S.2    Long, J.3    Zheng, W.4    Zhao, Z.5
  • 59
    • 77953957633 scopus 로고    scopus 로고
    • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    • Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010, 465:1033-1038.
    • (2010) Nature , vol.465 , pp. 1033-1038
    • Poliseno, L.1    Salmena, L.2    Zhang, J.3    Carver, B.4    Haveman, W.J.5    Pandolfi, P.P.6
  • 63
    • 46449111382 scopus 로고    scopus 로고
    • Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
    • Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A. Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res 2008, 18:1150-1162.
    • (2008) Genome Res , vol.18 , pp. 1150-1162
    • Iossifov, I.1    Zheng, T.2    Baron, M.3    Gilliam, T.C.4    Rzhetsky, A.5
  • 66
    • 73649123907 scopus 로고    scopus 로고
    • Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1
    • Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010, 17:98-110.
    • (2010) Cancer Cell , vol.17 , pp. 98-110
    • Verhaak, R.G.1    Hoadley, K.A.2    Purdom, E.3    Wang, V.4    Qi, Y.5    Wilkerson, M.D.6    Miller, C.R.7    Ding, L.8    Golub, T.9    Mesirov, J.P.10
  • 68
    • 71149117622 scopus 로고    scopus 로고
    • Metabolic systems biology
    • Palsson B. Metabolic systems biology. FEBS Lett 2009, 583:3900-3904.
    • (2009) FEBS Lett , vol.583 , pp. 3900-3904
    • Palsson, B.1
  • 70
    • 36248940715 scopus 로고    scopus 로고
    • Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism
    • Nemenman I, Escola GS, Hlavacek WS, Unkefer PJ, Unkefer CJ, Wall ME. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Ann N Y Acad Sci 2007, 1115:102-115.
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 102-115
    • Nemenman, I.1    Escola, G.S.2    Hlavacek, W.S.3    Unkefer, P.J.4    Unkefer, C.J.5    Wall, M.E.6
  • 79
  • 84
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
    • Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 2000:418-429.
    • (2000) Pac Symp Biocomput , pp. 418-429
    • Butte, A.J.1    Kohane, I.S.2
  • 85
  • 86
    • 0038444122 scopus 로고    scopus 로고
    • Genome-wide In silico identification of transcriptional regulators controlling the cell cycle in human cells
    • Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y. Genome-wide In silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 2003, 13:773-780.
    • (2003) Genome Res , vol.13 , pp. 773-780
    • Elkon, R.1    Linhart, C.2    Sharan, R.3    Shamir, R.4    Shiloh, Y.5
  • 87
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 88
    • 0037722938 scopus 로고    scopus 로고
    • Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
    • Zeitlinger J, Simon I, Harbison CT, Hannett NM, Volkert TL, Fink GR, Young RA. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 2003, 113:395.
    • (2003) Cell , vol.113 , pp. 395
    • Zeitlinger, J.1    Simon, I.2    Harbison, C.T.3    Hannett, N.M.4    Volkert, T.L.5    Fink, G.R.6    Young, R.A.7
  • 89
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:166-176.
    • (2003) Nat Genet , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 94
    • 33748587841 scopus 로고    scopus 로고
    • A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes
    • Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 2006, 126:1203-1217.
    • (2006) Cell , vol.126 , pp. 1203-1217
    • Miranda, K.C.1    Huynh, T.2    Tay, Y.3    Ang, Y.S.4    Tam, W.L.5    Thomson, A.M.6    Lim, B.7    Rigoutsos, I.8
  • 98
    • 77955930508 scopus 로고    scopus 로고
    • Interaction proteomics: characterization of protein complexes using tandem affinity purification-mass spectrometry
    • Volkel P, Le Faou P, Angrand PO. Interaction proteomics: characterization of protein complexes using tandem affinity purification-mass spectrometry. Biochem Soc Trans 2010, 38:883-887.
    • (2010) Biochem Soc Trans , vol.38 , pp. 883-887
    • Volkel, P.1    Le Faou, P.2    Angrand, P.O.3
  • 100
    • 53749102828 scopus 로고    scopus 로고
    • Network-based model weighting to detect multiple loci influencing complex diseases
    • Pan W. Network-based model weighting to detect multiple loci influencing complex diseases. Hum Genet 2008, 124:225-234.
    • (2008) Hum Genet , vol.124 , pp. 225-234
    • Pan, W.1


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