메뉴 건너뛰기




Volumn 41, Issue 1, 2013, Pages

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL DIFFERENTIATION; CELL STRAIN HL 60; CELLULAR PHENOTYPE; COMPUTER MODEL; EPITHELIAL MESENCHYMAL TRANSITION; EVOLUTIONARY ALGORITHM; GENE EXPRESSION; GENE INTERACTION; GENE REGULATORY NETWORK; GENETIC STABILITY; HUMAN; HUMAN CELL; INFORMATION SCIENCE; INTERNAL CONSISTENCY; MESODERM; NEUTROPHIL; OSTEOBLAST; PHENOTYPE; POSITIVE FEEDBACK; PREDICTIVE VALIDITY; PRIORITY JOURNAL; PROBABILITY; PROCESS OPTIMIZATION; STEM CELL;

EID: 84871764162     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks785     Document Type: Article
Times cited : (26)

References (50)
  • 3
    • 62549089350 scopus 로고    scopus 로고
    • Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
    • Huang, A.C., Hu, L., Kauffman, S.A., Zhang, W. and Shmulevich, I. (2009) Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst. Biol., 3, 20.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 20
    • Huang, A.C.1    Hu, L.2    Kauffman, S.A.3    Zhang, W.4    Shmulevich, I.5
  • 4
    • 17644427718 scopus 로고    scopus 로고
    • Causal protein-signaling networks derived from multiparameter single-cell data
    • Sachs, K., Perez, O., Pe'er, D., Lauffenburger, D.A. and Nolan, G.P. (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science, 308, 523-529.
    • (2005) Science , vol.308 , pp. 523-529
    • Sachs, K.1    Perez, O.2    Pe'Er, D.3    Lauffenburger, D.A.4    Nolan, G.P.5
  • 6
    • 3242882981 scopus 로고    scopus 로고
    • Chain functions and scoring functions in genetic networks
    • Gat-Viks, I. and Shamir, R. (2003) Chain functions and scoring functions in genetic networks. Bioinformatics, 19(Suppl. 1), i108-i117.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Gat-Viks, I.1    Shamir, R.2
  • 7
  • 8
    • 12844254468 scopus 로고    scopus 로고
    • Modeling and analysis of heterogeneous regulation in biological networks
    • Gat-Viks, I., Tanay, A. and Shamir, R. (2004) Modeling and analysis of heterogeneous regulation in biological networks. J. Comput. Biol. J. Comput. Mol. Cell Biol., 11, 1034-1049.
    • (2004) J. Comput. Biol. J. Comput. Mol. Cell Biol. , vol.11 , pp. 1034-1049
    • Gat-Viks, I.1    Tanay, A.2    Shamir, R.3
  • 9
    • 79951531878 scopus 로고    scopus 로고
    • From biological pathways to regulatory networks
    • Layek, R.K., Datta, A. and Dougherty, E.R. (2011) From biological pathways to regulatory networks. Mol. bioSyst., 7, 843-851.
    • (2011) Mol. BioSyst. , vol.7 , pp. 843-851
    • Layek, R.K.1    Datta, A.2    Dougherty, E.R.3
  • 10
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman, S.A. (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol, 22, 437.
    • (1969) J. Theor. Biol , vol.22 , pp. 437
    • Kauffman, S.A.1
  • 11
    • 0004161153 scopus 로고
    • Oxford University Press, New York
    • Kauffman, S.A. (1993) The Origins of Order. Oxford University Press, New York, 1993.
    • (1993) The Origins of Order , vol.1993
    • Kauffman, S.A.1
  • 12
    • 18144408736 scopus 로고    scopus 로고
    • Cell fates as high-dimensional attractor states of a complex gene regulatory network
    • Huang, S., Eichler, G., Bar-Yam, Y. and Ingber, D.E. (2005) Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev. Lett., 94, 128701.
    • (2005) Phys Rev. Lett. , vol.94 , pp. 128701
    • Huang, S.1    Eichler, G.2    Bar-Yam, Y.3    Ingber, D.E.4
  • 13
    • 50549088838 scopus 로고    scopus 로고
    • Synchronous versus asynchronous modeling of gene regulatory networks
    • Garg, A., Di Cara, A., Xenarios, I., Mendoza, L. and De Micheli, G. (2008) Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics, 24, 1917-1925.
    • (2008) Bioinformatics , vol.24 , pp. 1917-1925
    • Garg, A.1    Di Cara, A.2    Xenarios, I.3    Mendoza, L.4    De Micheli, G.5
  • 14
    • 84871766785 scopus 로고    scopus 로고
    • An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experimentsresearch in computational molecular biology
    • Speed, T. and Huang, H. (eds) Springer Berlin, Heidelberg
    • Garg, A., Xenarios, I., Mendoza, L. and DeMicheli, G. (2007) An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experimentsresearch in computational molecular biology. In: Speed, T. and Huang, H. (eds), Lecture Notes in Computer Science, Vol. 4453. Springer Berlin, Heidelberg, pp., pp-76.
    • (2007) Lecture Notes in Computer Science , vol.4453 , pp. 76
    • Garg, A.1    Xenarios, I.2    Mendoza, L.3    Demicheli, G.4
  • 15
    • 77952851181 scopus 로고    scopus 로고
    • BoolNet-an R package for generation, reconstruction and analysis of Boolean networks
    • Mussel, C., Hopfensitz, M. and Kestler, H.A. (2010) BoolNet-an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics, 26, 1378-1380.
    • (2010) Bioinformatics , vol.26 , pp. 1378-1380
    • Mussel, C.1    Hopfensitz, M.2    Kestler, H.A.3
  • 16
    • 33646352954 scopus 로고    scopus 로고
    • GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks
    • Gonzalez, A.G., Naldi, A., Sanchez, L., Thieffry, D. and Chaouiya, C. (2006) GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Bio Systems, 84, 91-100.
    • (2006) Bio Systems , vol.84 , pp. 91-100
    • Gonzalez, A.G.1    Naldi, A.2    Sanchez, L.3    Thieffry, D.4    Chaouiya, C.5
  • 17
    • 0029267491 scopus 로고
    • Dynamical behavior of biological regulatory networks.1. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
    • Thomas, R., Thieffry, D. and Kaufman, M. (1995) Dynamical behavior of biological regulatory networks.1. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Mathemat. Biol., 57, 247-276.
    • (1995) Bull. Mathemat. Biol. , vol.57 , pp. 247-276
    • Thomas, R.1    Thieffry, D.2    Kaufman, M.3
  • 19
    • 33646346114 scopus 로고    scopus 로고
    • A method for the generation of standardized qualitative dynamical systems of regulatory networks
    • Mendoza, L. and Xenarios, I. (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Modelling, 3, 13.
    • (2006) Theor. Biol. Med. Modelling , vol.3 , pp. 13
    • Mendoza, L.1    Xenarios, I.2
  • 21
    • 0031800433 scopus 로고    scopus 로고
    • Laws for the dynamics of regulatory networks
    • Thomas, R. (1998) Laws for the dynamics of regulatory networks. Int. J. Dev. Biol., 42, 479-485.
    • (1998) Int. J. Dev. Biol. , vol.42 , pp. 479-485
    • Thomas, R.1
  • 23
    • 84871810475 scopus 로고    scopus 로고
    • Regulatory networks and in-silico gene perturbation experiments
    • Springer, Berlin, Heidelberg Lect. Notes Comput. Sci., 4453, 62-76
    • Speed, T.H.H. (2007) Regulatory networks and in-silico gene perturbation experiments. Research in Computational Molecular Biology. Springer Berlin, Heidelberg, pp. 62-76. Lect. Notes Comput. Sci., 4453, 62-76.
    • (2007) Research in Computational Molecular Biology , pp. 62-76
    • Speed, T.H.H.1
  • 24
    • 0001909598 scopus 로고
    • Finding all the elementary circuits of a directed graph
    • Johnson, D.B. (1975) Finding all the elementary circuits of a directed graph. SIAM J. Comput., 4, 77-84.
    • (1975) SIAM J. Comput. , vol.4 , pp. 77-84
    • Johnson, D.B.1
  • 27
    • 0018698475 scopus 로고
    • Characterization of the continuous, differentiating myeloid cell line (HL-60) from a patient with acute promyelocytic leukemia
    • Gallagher, R., Collins, S., Trujillo, J., McCredie, K., Ahearn, M., Tsai, S., Metzgar, R., Aulakh, G., Ting, R., Ruscetti, F. et al. (1979) Characterization of the continuous, differentiating myeloid cell line (HL-60) from a patient with acute promyelocytic leukemia. Blood, 54, 713-733.
    • (1979) Blood , vol.54 , pp. 713-733
    • Gallagher, R.1    Collins, S.2    Trujillo, J.3    McCredie, K.4    Ahearn, M.5    Tsai, S.6    Metzgar, R.7    Aulakh, G.8    Ting, R.9    Ruscetti, F.10
  • 28
    • 45449097039 scopus 로고    scopus 로고
    • Differential gene expression patterns coupled to commitment and acquisition of phenotypic hallmarks during neutrophil differentiation of human leukaemia HL-60 cells
    • Mollinedo, F., Lopez-Perez, R. and Gajate, C. (2008) Differential gene expression patterns coupled to commitment and acquisition of phenotypic hallmarks during neutrophil differentiation of human leukaemia HL-60 cells. Gene, 419, 16-26.
    • (2008) Gene , vol.419 , pp. 16-26
    • Mollinedo, F.1    Lopez-Perez, R.2    Gajate, C.3
  • 30
    • 0037452973 scopus 로고    scopus 로고
    • Identification of genes responsible for osteoblast differentiation from human mesodermal progenitor cells
    • Qi, H., Aguiar, D.J., Williams, S.M., La Pean, A., Pan, W. and Verfaillie, C.M. (2003) Identification of genes responsible for osteoblast differentiation from human mesodermal progenitor cells. Proc. Natl Acad. Sci. USA, 100, 3305-3310.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 3305-3310
    • Qi, H.1    Aguiar, D.J.2    Williams, S.M.3    La Pean, A.4    Pan, W.5    Verfaillie, C.M.6
  • 31
    • 0141515736 scopus 로고    scopus 로고
    • MedScan, a natural language processing engine for MEDLINE abstracts
    • Novichkova, S., Egorov, S. and Daraselia, N. (2003) MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics, 19, 1699-1706.
    • (2003) Bioinformatics , vol.19 , pp. 1699-1706
    • Novichkova, S.1    Egorov, S.2    Daraselia, N.3
  • 32
    • 1842559914 scopus 로고    scopus 로고
    • Extracting human protein interactions from MEDLINE using a full-sentence parser
    • Daraselia, N., Yuryev, A., Egorov, S., Novichkova, S., Nikitin, A. and Mazo, I. (2004) Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics, 20, 604-611.
    • (2004) Bioinformatics , vol.20 , pp. 604-611
    • Daraselia, N.1    Yuryev, A.2    Egorov, S.3    Novichkova, S.4    Nikitin, A.5    Mazo, I.6
  • 34
    • 4444311806 scopus 로고    scopus 로고
    • A proposal for using the ensemble approach to understand genetic regulatory networks
    • Kauffman, S. (2004) A proposal for using the ensemble approach to understand genetic regulatory networks. J. Theor. Biol., 230, 581-590.
    • (2004) J. Theor. Biol. , vol.230 , pp. 581-590
    • Kauffman, S.1
  • 35
    • 82255196116 scopus 로고    scopus 로고
    • Interferon regulatory factor-1 binds c-Cbl, enhances mitogen activated protein kinase signaling and promotes retinoic acid-induced differentiation of HL-60 human myelo-monoblastic leukemia cells
    • Shen, M., Bunaciu, R.P., Congleton, J., Jensen, H.A., Sayam, L.G., Varner, J.D. and Yen, A. (2011) Interferon regulatory factor-1 binds c-Cbl, enhances mitogen activated protein kinase signaling and promotes retinoic acid-induced differentiation of HL-60 human myelo-monoblastic leukemia cells. Leukemia Lymphoma, 52, 2372-2379.
    • (2011) Leukemia Lymphoma , vol.52 , pp. 2372-2379
    • Shen, M.1    Bunaciu, R.P.2    Congleton, J.3    Jensen, H.A.4    Sayam, L.G.5    Varner, J.D.6    Yen, A.7
  • 37
    • 67650045932 scopus 로고    scopus 로고
    • A twist-snail axis critical for TrkB-induced epithelial-mesenchymal transition-like transformation, anoikis resistance, and metastasis
    • Smit, M.A., Geiger, T.R., Song, J.Y., Gitelman, I. and Peeper, D.S. (2009) A twist-snail axis critical for TrkB-induced epithelial-mesenchymal transition-like transformation, anoikis resistance, and metastasis. Mol. Cell. Biol., 29, 3722-3737.
    • (2009) Mol. Cell. Biol. , vol.29 , pp. 3722-3737
    • Smit, M.A.1    Geiger, T.R.2    Song, J.Y.3    Gitelman, I.4    Peeper, D.S.5
  • 38
    • 84857495668 scopus 로고    scopus 로고
    • Cooperation of p300 and PCAF in the control of microRNA 200c/141 transcription and epithelial characteristics
    • Mizuguchi, Y., Specht, S., Lunz, J.G. 3rd, Isse, K., Corbitt, N., Takizawa, T. and Demetris, A.J. (2012) Cooperation of p300 and PCAF in the control of microRNA 200c/141 transcription and epithelial characteristics. PloS One, 7, e32449.
    • (2012) PloS One , vol.7
    • Mizuguchi, Y.1    Specht, S.2    Lunz III, J.G.3    Isse, K.4    Corbitt, N.5    Takizawa, T.6    Demetris, A.J.7
  • 39
    • 48149110985 scopus 로고    scopus 로고
    • IL-6 receptor expression and IL-6 effects change during osteoblast differentiation
    • Li, Y., Backesjo, C.M., Haldosen, L.A. and Lindgren, U. (2008) IL-6 receptor expression and IL-6 effects change during osteoblast differentiation. Cytokine, 43, 165-173.
    • (2008) Cytokine , vol.43 , pp. 165-173
    • Li, Y.1    Backesjo, C.M.2    Haldosen, L.A.3    Lindgren, U.4
  • 41
    • 0034014914 scopus 로고    scopus 로고
    • Production and action of transforming growth factor-beta in human osteoblast cultures: Dependence on cell differentiation and modulation by calcitriol
    • Kassem, M., Kveiborg, M. and Eriksen, E.F. (2000) Production and action of transforming growth factor-beta in human osteoblast cultures: dependence on cell differentiation and modulation by calcitriol. Eur. J. Clin. Invest., 30, 429-437.
    • (2000) Eur. J. Clin. Invest. , vol.30 , pp. 429-437
    • Kassem, M.1    Kveiborg, M.2    Eriksen, E.F.3
  • 42
    • 0001679798 scopus 로고
    • Induction of differentiation of the human promyelocytic leukemia cell line (HL-60) by retinoic acid
    • Breitman, T.R., Selonick, S.E. and Collins, S.J. (1980) Induction of differentiation of the human promyelocytic leukemia cell line (HL-60) by retinoic acid. Proc. Natl Acad. Sci. USA, 77, 2936-2940.
    • (1980) Proc. Natl Acad. Sci. USA , vol.77 , pp. 2936-2940
    • Breitman, T.R.1    Selonick, S.E.2    Collins, S.J.3
  • 43
    • 0001718811 scopus 로고
    • Terminal differentiation of human promyelocytic leukemia cells induced by dimethyl sulfoxide and other polar compounds
    • Collins, S.J., Ruscetti, F.W., Gallagher, R.E. and Gallo, R.C. (1978) Terminal differentiation of human promyelocytic leukemia cells induced by dimethyl sulfoxide and other polar compounds. Proc. Natl Acad. Sci. USA, 75, 2458-2462.
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 2458-2462
    • Collins, S.J.1    Ruscetti, F.W.2    Gallagher, R.E.3    Gallo, R.C.4
  • 44
    • 0020577903 scopus 로고
    • 1, 25-dihydroxyvitamin D3 inhibits proliferation of human promyelocytic leukaemia (HL60) cells and induces monocyte-macrophage differentiation in HL60 and normal human bone marrow cells
    • McCarthy, D.M., San Miguel, J.F., Freake, H.C., Green, P.M., Zola, H., Catovsky, D. and Goldman, J.M. (1983) 1, 25-dihydroxyvitamin D3 inhibits proliferation of human promyelocytic leukaemia (HL60) cells and induces monocyte-macrophage differentiation in HL60 and normal human bone marrow cells. Leukemia Res., 7, 51-55.
    • (1983) Leukemia Res. , vol.7 , pp. 51-55
    • McCarthy, D.M.1    San Miguel, J.F.2    Freake, H.C.3    Green, P.M.4    Zola, H.5    Catovsky, D.6    Goldman, J.M.7
  • 45
    • 0002966839 scopus 로고
    • Human promyelocytic leukemia cells in culture differentiate into macrophage-like cells when treated with a phorbol diester
    • Rovera, G., Santoli, D. and Damsky, C. (1979) Human promyelocytic leukemia cells in culture differentiate into macrophage-like cells when treated with a phorbol diester. Proc. Natl Acad. Sci. USA, 76, 2779-2783.
    • (1979) Proc. Natl Acad. Sci. USA , vol.76 , pp. 2779-2783
    • Rovera, G.1    Santoli, D.2    Damsky, C.3
  • 46
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.L. and Ideker, T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 48
    • 0022637718 scopus 로고
    • Biosynthetic (recombinant) human granulocyte-macrophage colony-stimulating factor: Effect on normal bone marrow and leukemia cell lines
    • Tomonaga, M., Golde, D.W. and Gasson, J.C. (1986) Biosynthetic (recombinant) human granulocyte-macrophage colony-stimulating factor: effect on normal bone marrow and leukemia cell lines. Blood, 67, 31-36.
    • (1986) Blood , vol.67 , pp. 31-36
    • Tomonaga, M.1    Golde, D.W.2    Gasson, J.C.3
  • 49
    • 0031623453 scopus 로고    scopus 로고
    • Efficient State Classification of Finite State Markov Chains
    • Xie AaB, P.A. (1998) Efficient State Classification of Finite State Markov Chains. Proc of DAC, 1998.
    • (1998) Proc of DAC, 1998
    • Xie Aab, P.A.1
  • 50
    • 40749087306 scopus 로고    scopus 로고
    • BiNoM: A Cytoscape plugin for manipulating and analyzing biological networks
    • Zinovyev, A., Viara, E., Calzone, L. and Barillot, E. (2008) BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics, 24, 876-877.
    • (2008) Bioinformatics , vol.24 , pp. 876-877
    • Zinovyev, A.1    Viara, E.2    Calzone, L.3    Barillot, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.