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Volumn 19, Issue 2, 2012, Pages 188-199

Dynamic modeling of miRNA-mediated feed-forward loops

Author keywords

biochemical networks; computational molecular biology

Indexed keywords

MESSENGER RNA; MICRORNA; TRANSCRIPTION FACTOR;

EID: 84856763727     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0274     Document Type: Article
Times cited : (7)

References (42)
  • 1
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • DOI 10.1038/nrg2102, PII NRG2102
    • Alon, U. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461. (Pubitemid 46789247)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.6 , pp. 450-461
    • Alon, U.1
  • 2
    • 49949116902 scopus 로고    scopus 로고
    • The impact of microRNAs on protein output
    • Baek, D., Villen, J., Shin, C., et al. 2008. The impact of microRNAs on protein output. Nature 455, 64-71.
    • (2008) Nature , vol.455 , pp. 64-71
    • Baek, D.1    Villen, J.2    Shin, C.3
  • 3
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D.P. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel, D.P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 34548200846 scopus 로고    scopus 로고
    • DAISY: A new software tool to test global identifiability of biological and physiological systems
    • DOI 10.1016/j.cmpb.2007.07.002, PII S0169260707001605
    • Bellu, G., Saccomani, M.P., Audoly, S., et al. 2007. DAISY: a new software tool to test global identifiability of biological and physiological systems. Comput. Methods Programs Biomed. 88, 52-61. (Pubitemid 47331951)
    • (2007) Computer Methods and Programs in Biomedicine , vol.88 , Issue.1 , pp. 52-61
    • Bellu, G.1    Saccomani, M.P.2    Audoly, S.3    D'Angio, L.4
  • 7
    • 4444339832 scopus 로고    scopus 로고
    • Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
    • Chen, H.C., Lee, H.C., Lin, T.Y., et al. 2004. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 20, 1914-1927.
    • (2004) Bioinformatics , vol.20 , pp. 1914-1927
    • Chen, H.C.1    Lee, H.C.2    Lin, T.Y.3
  • 8
    • 20844452570 scopus 로고    scopus 로고
    • A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
    • Chen, K.C., Wang, T.Y., Tseng, H.H., et al. 2005. A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics 21, 2883-2890.
    • (2005) Bioinformatics , vol.21 , pp. 2883-2890
    • Chen, K.C.1    Wang, T.Y.2    Tseng, H.H.3
  • 10
    • 28044455435 scopus 로고    scopus 로고
    • MicroPrimer: The biogenesis and function of microRNA
    • DOI 10.1242/dev.02070
    • Du, T., and Zamore, P.D. 2005. microPrimer: the biogenesis and function of microRNA. Development 132, 4645-4652. (Pubitemid 41685275)
    • (2005) Development , vol.132 , Issue.21 , pp. 4645-4652
    • Du, T.1    Zamore, P.D.2
  • 11
    • 79952289884 scopus 로고    scopus 로고
    • A curated database of miRNA-mediated feed-forward loops involving MYC as master regulator
    • El Baroudi, M., Cora, D., Bosia, C., et al. 2011. A curated database of miRNA-mediated feed-forward loops involving MYC as master regulator. PLoS ONE 6, e14742.
    • (2011) PLoS ONE , vol.6
    • El Baroudi, M.1    Cora, D.2    Bosia, C.3
  • 12
    • 77956520986 scopus 로고    scopus 로고
    • CircuitsDB: A database of mixed microRNA/transcription factor feedforward regulatory circuits in human and mouse
    • Friard, O., Re, A., Taverna, D., et al. 2010. CircuitsDB: a database of mixed microRNA/transcription factor feedforward regulatory circuits in human and mouse. BMC Bioinform. 11, 435.
    • (2010) BMC Bioinform. , vol.11 , pp. 435
    • Friard, O.1    Re, A.2    Taverna, D.3
  • 13
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman, R.C., Farh, K.K., Burge, C.B., et al. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105.
    • (2009) Genome Res , vol.19 , pp. 92-105
    • Friedman, R.C.1    Farh, K.K.2    Burge, C.B.3
  • 15
    • 84984765621 scopus 로고    scopus 로고
    • Canalization of development by microRNAs
    • Hornstein, E., and Shomron, N. 2006. Canalization of development by microRNAs. Nat. Genet. 38, S20-S24.
    • (2006) Nat. Genet , vol.38
    • Hornstein, E.1    Shomron, N.2
  • 16
    • 58149179989 scopus 로고    scopus 로고
    • MiR2Disease: A manually curated database for microRNA deregulation in human disease
    • Jiang, Q., Wang, Y., Hao, Y., et al. 2009. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 37, D98-D104.
    • (2009) Nucleic Acids Res , vol.37
    • Jiang, Q.1    Wang, Y.2    Hao, Y.3
  • 17
    • 77349121900 scopus 로고    scopus 로고
    • Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data
    • Jung, C.H., Hansen, M.A., Makunin, I.V., et al. 2010. Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. BMC Genomics 11, 77.
    • (2010) BMC Genomics , vol.11 , pp. 77
    • Jung, C.H.1    Hansen, M.A.2    Makunin, I.V.3
  • 18
    • 33746428728 scopus 로고    scopus 로고
    • A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
    • 2005.0006
    • Kalir, S., Mangan, S., and Alon, U. 2005. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol. Syst. Biol. 1, 2005.0006.
    • (2005) Mol. Syst. Biol , vol.1
    • Kalir, S.1    Mangan, S.2    Alon, U.3
  • 19
    • 47349095809 scopus 로고    scopus 로고
    • The incoherent feed-forward loop can generate non-monotonic input functions for genes
    • Kaplan, S., Bren, A., Dekel, E., et al. 2008. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol. Syst. Biol. 4, 203.
    • (2008) Mol. Syst. Biol , vol.4 , pp. 203
    • Kaplan, S.1    Bren, A.2    Dekel, E.3
  • 20
    • 70350125874 scopus 로고    scopus 로고
    • MicroRNA miR-27b impairs human adipocyte differentiation and targets PPARgamma
    • Karbiener, M., Fischer, C., Nowitsch, S., et al. 2009. microRNA miR-27b impairs human adipocyte differentiation and targets PPARgamma. Biochem. Biophys. Res. Commun. 390, 247-251.
    • (2009) Biochem. Biophys. Res. Commun. , vol.390 , pp. 247-251
    • Karbiener, M.1    Fischer, C.2    Nowitsch, S.3
  • 21
    • 41349120349 scopus 로고    scopus 로고
    • Computational modeling of post-transcriptional gene regulation by microRNAs
    • DOI 10.1089/cmb.2007.0184
    • Khanin, R., and Vinciotti, V. 2008. Computational modeling of post-transcriptional gene regulation by microRNAs. J. Comput. Biol. 15, 305-316. (Pubitemid 351450464)
    • (2008) Journal of Computational Biology , vol.15 , Issue.3 , pp. 305-316
    • Khanin, R.1    Vinciotti, V.2
  • 22
    • 0035955374 scopus 로고    scopus 로고
    • Identification of novel genes coding for small expressed RNAs
    • DOI 10.1126/science.1064921
    • Lagos-Quintana, M., Rauhut, R., Lendeckel, W., et al. 2001. Identification of novel genes coding for small expressed RNAs. Science 294, 853-858. (Pubitemid 33032103)
    • (2001) Science , vol.294 , Issue.5543 , pp. 853-858
    • Lagos-Quintana, M.1    Rauhut, R.2    Lendeckel, W.3    Tuschl, T.4
  • 24
    • 36849064251 scopus 로고    scopus 로고
    • Target-specific and global effectors in gene regulation by microRNA
    • DOI 10.1529/biophysj.107.118448
    • Levine, E., Ben Jacob, E., and Levine, H. 2007a. Target-specific and global effectors in gene regulation by MicroRNA. Biophys. J. 93, L52-4. (Pubitemid 350223788)
    • (2007) Biophysical Journal , vol.93 , Issue.11
    • Levine, E.1    Jacob, E.B.2    Levine, H.3
  • 25
    • 34548668642 scopus 로고    scopus 로고
    • Quantitative characteristics of gene regulation by small RNA
    • Levine, E., Zhang, Z., Kuhlman, T., et al. 2007b. Quantitative characteristics of gene regulation by small RNA. PLoS Biol. 5, e229.
    • (2007) PLoS Biol , vol.5
    • Levine, E.1    Zhang, Z.2    Kuhlman, T.3
  • 26
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • DOI 10.1016/j.cell.2004.12.035, PII S0092867404012607
    • Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. (Pubitemid 40094598)
    • (2005) Cell , vol.120 , Issue.1 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 27
  • 28
    • 64249144494 scopus 로고    scopus 로고
    • A microRNA imparts robustness against environmental fluctuation during development
    • Li, X., Cassidy, J.J., Reinke, C.A., et al. 2009. A microRNA imparts robustness against environmental fluctuation during development. Cell 137, 273-282.
    • (2009) Cell , vol.137 , pp. 273-282
    • Li, X.1    Cassidy, J.J.2    Reinke, C.A.3
  • 29
    • 71049182983 scopus 로고    scopus 로고
    • Specialized or flexible feed-forward loop motifs: A question of topology
    • Macia, J., Widder, S., and Sole, R. 2009. Specialized or flexible feed-forward loop motifs: a question of topology. BMC Syst. Biol. 3, 84.
    • (2009) BMC Syst. Biol , vol.3 , pp. 84
    • MacIa, J.1    Widder, S.2    Sole, R.3
  • 31
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • DOI 10.1126/science.298.5594.824
    • Milo, R., Shen-Orr, S., Itzkovitz, S., et al. 2002. Network motifs: simple building blocks of complex networks. Science 298, 824-827. (Pubitemid 35231534)
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 32
    • 79952302623 scopus 로고    scopus 로고
    • The role of incoherent microRNA-mediated feedforward loops in noise buffering
    • Osella, M., Bosia, C., Corà, D., et al. 2011. The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput. Biol. 7, e1001101.
    • (2011) PLoS Comput. Biol. , vol.7
    • Osella, M.1    Bosia, C.2    Corà, D.3
  • 33
    • 70349334678 scopus 로고    scopus 로고
    • Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human
    • Re, A., Cora, D., Taverna, D., et al. 2009. Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Mol. Biosyst. 5, 854-867.
    • (2009) Mol. Biosyst , vol.5 , pp. 854-867
    • Re, A.1    Cora, D.2    Taverna, D.3
  • 34
    • 48549087683 scopus 로고    scopus 로고
    • Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
    • Scheideler, M., Elabd, C., Zaragosi, L.E., et al. 2008. Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. BMC Genomics 9, 340.
    • (2008) BMC Genomics , vol.9 , pp. 340
    • Scheideler, M.1    Elabd, C.2    Zaragosi, L.E.3
  • 35
    • 49949117302 scopus 로고    scopus 로고
    • Widespread changes in protein synthesis induced by microRNAs
    • Selbach, M., Schwanhausser, B., Thierfelder, N., et al. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63.
    • (2008) Nature , vol.455 , pp. 58-63
    • Selbach, M.1    Schwanhausser, B.2    Thierfelder, N.3
  • 36
    • 34547555796 scopus 로고    scopus 로고
    • Global and local architecture of the mammalian microRNA-transcription factor regulatory network
    • Shalgi, R., Lieber, D., Oren, M., et al. 2007. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. 3, e131.
    • (2007) PLoS Comput. Biol , vol.3
    • Shalgi, R.1    Lieber, D.2    Oren, M.3
  • 37
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S.S., Milo, R., Mangan, S., et al. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68.
    • (2002) Nat. Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3
  • 38
    • 34748871477 scopus 로고    scopus 로고
    • Regulation of gene expression by small non-coding RNAs: A quantitative view
    • Shimoni, Y., Friedlander, G., Hetzroni, G., et al. 2007. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol. 3, 138.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 138
    • Shimoni, Y.1    Friedlander, G.2    Hetzroni, G.3
  • 39
    • 34249819336 scopus 로고    scopus 로고
    • MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals
    • DOI 10.1016/j.molcel.2007.05.018, PII S109727650700319X
    • Tsang, J., Zhu, J., and van Oudenaarden, A. 2007. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell 26, 753-767. (Pubitemid 46856248)
    • (2007) Molecular Cell , vol.26 , Issue.5 , pp. 753-767
    • Tsang, J.1    Zhu, J.2    Van Oudenaarden, A.3
  • 40
    • 77955840320 scopus 로고    scopus 로고
    • Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation
    • Vohradsky, J., Panek, J., and Vomastek, T. 2010. Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation. Nucleic Acids Res. 38, 4579-4585.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4579-4585
    • Vohradsky, J.1    Panek, J.2    Vomastek, T.3
  • 41
    • 33846703173 scopus 로고    scopus 로고
    • Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae
    • DOI 10.1093/nar/gkl1001
    • Vu, T.T., and Vohradsky, J. 2007. Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic Acids Res. 35, 279-287. (Pubitemid 46189852)
    • (2007) Nucleic Acids Research , vol.35 , Issue.1 , pp. 279-287
    • Vu, T.T.1    Vohradsky, J.2
  • 42
    • 66049153398 scopus 로고    scopus 로고
    • Evolution under canalization and the dual roles of microRNAs: A hypothesis
    • Wu, C.I., Shen, Y., and Tang, T. 2009. Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res. 19, 734-743.
    • (2009) Genome Res , vol.19 , pp. 734-743
    • Wu, C.I.1    Shen, Y.2    Tang, T.3


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