메뉴 건너뛰기




Volumn 774, Issue , 2013, Pages 55-76

MicroRNA-regulated networks: The Perfect Storm for classical molecular biology, the Ideal Scenario for systems biology

Author keywords

Bistability; Feedback loop; Feedforward loop; Kinetic models; MiRNA cluster; MiRNA network motifs; MiRNA regulated networks; MiRNA target hub; Post transcriptional regulation; Ultrasensitivity

Indexed keywords

MICRORNA; MICRORNA 93; PROTEIN P21; SIRTUIN 1; TRANSCRIPTION FACTOR E2F1; UNCLASSIFIED DRUG;

EID: 84934438006     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-7-5590-1_4     Document Type: Article
Times cited : (47)

References (70)
  • 1
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 2
    • 43349090926 scopus 로고    scopus 로고
    • MiRNAs: Effectors of environmental in fluences on gene expression and disease
    • Hudder A, Novak RF (2008) miRNAs: effectors of environmental in fluences on gene expression and disease. Toxicol Sci 103:228-240
    • (2008) Toxicol Sci , vol.103 , pp. 228-240
    • Hudder, A.1    Novak, R.F.2
  • 3
    • 61849137222 scopus 로고    scopus 로고
    • Many roads to maturity: MicroRNA biogenesis pathways and their regulation
    • Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11:228-234
    • (2009) Nat Cell Biol , vol.11 , pp. 228-234
    • Winter, J.1    Jung, S.2    Keller, S.3    Gregory, R.I.4    Diederichs, S.5
  • 4
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman RC, Farh KK-H, Burge CB, Bartel DP (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    Kk-H, F.2    Burge, C.B.3    Bartel, D.P.4
  • 5
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215-233
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 9
    • 58149186499 scopus 로고    scopus 로고
    • MiRecords: An integrated resource for microRNAtarget interactions
    • Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T (2009) miRecords: an integrated resource for microRNAtarget interactions. Nucleic Acids Res 37:D105-D110
    • (2009) Nucleic Acids Res , vol.37
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5    Li, T.6
  • 10
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal microRNA targets
    • Sethupathy P, Corda B, Hatzigeorgiou AG (2006) TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12:192-197
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 11
    • 79959805164 scopus 로고    scopus 로고
    • MiRWalk -Database prediction of possible MiRNA binding sites by 'walking' the genes of three genomes
    • Dweep H, Sticht C, Pandey P, Gretz N (2011) miRWalk -database: prediction of possible miRNA binding sites by 'walking' the genes of three genomes. J Biomed Inform 44:839-847
    • (2011) J Biomed Inform , vol.44 , pp. 839-847
    • Dweep, H.1    Sticht, C.2    Pandey, P.3    Gretz, N.4
  • 13
    • 75549092303 scopus 로고    scopus 로고
    • TransmiR: A transcription factor-microRNA regulation database
    • Wang J, Lu M, Qiu C, Cui Q (2010) TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res 38:D119-D122
    • (2010) Nucleic Acids Res , vol.38
    • Wang, J.1    Lu, M.2    Qiu, C.3    Cui, Q.4
  • 14
    • 77950820292 scopus 로고    scopus 로고
    • PuTmiR: A database for extracting neighboring transcription factors of human microRNAs
    • Bandyopadhyay S, Bhattacharyya M (2010) PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics 11:190
    • (2010) BMC Bioinformatics , vol.11 , pp. 190
    • Bandyopadhyay, S.1    Bhattacharyya, M.2
  • 17
    • 77951985216 scopus 로고    scopus 로고
    • Examination of the expanding pathways for the regulation of p21 expression and activity
    • Jung Y-S, Qian Y, Chen X (2010) Examination of the expanding pathways for the regulation of p21 expression and activity. Cell Signal 22:1003-1012
    • (2010) Cell Signal , vol.22 , pp. 1003-1012
    • Jung, Y.-S.1    Qian, Y.2    Chen, X.3
  • 18
    • 0033080402 scopus 로고    scopus 로고
    • Transcriptional regulation of the p21((WAF1/CIP1)) gene
    • Gartel AL, Tyner AL (1999) Transcriptional regulation of the p21((WAF1/CIP1)) gene. Exp Cell Res 246:280-289
    • (1999) Exp Cell Res , vol.246 , pp. 280-289
    • Gartel, A.L.1    Tyner, A.L.2
  • 19
    • 67649424560 scopus 로고    scopus 로고
    • P21 in cancer: Intricate networks and multiple activities
    • Abbas T, Dutta A (2009) p21 in cancer: intricate networks and multiple activities. Nat Rev Cancer 9:400-414
    • (2009) Nat Rev Cancer , vol.9 , pp. 400-414
    • Abbas, T.1    Dutta, A.2
  • 20
    • 77951092028 scopus 로고    scopus 로고
    • Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region
    • Wu S, Huang S, Ding J, Zhao Y, Liang L, Liu T, Zhan R, He X (2010) Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region. Oncogene 29:2302-2308
    • (2010) Oncogene , vol.29 , pp. 2302-2308
    • Wu, S.1    Huang, S.2    Ding, J.3    Zhao, Y.4    Liang, L.5    Liu, T.6    Zhan, R.7    He, X.8
  • 22
    • 77957928119 scopus 로고    scopus 로고
    • Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models
    • Vera J, Rath O, Balsa-Canto E, Banga JR, Kolch W, Wolkenhauer O (2010) Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models. Mol Biosyst 6:2174-2191
    • (2010) Mol Biosyst , vol.6 , pp. 2174-2191
    • Vera, J.1    Rath, O.2    Balsa-Canto, E.3    Banga, J.R.4    Kolch, W.5    Wolkenhauer, O.6
  • 23
    • 84859994220 scopus 로고    scopus 로고
    • Comput ational approaches for analyzing information flow in biological networks
    • Kholodenko B, Yaffe MB, Kolch W (2012) Comput ational approaches for analyzing information flow in biological networks. Sci Signal 5:re1
    • (2012) Sci Signal , vol.5
    • Kholodenko, B.1    Yaffe, M.B.2    Kolch, W.3
  • 25
    • 59049094552 scopus 로고    scopus 로고
    • A system biology approach to understand functional activity of cell communication systems
    • Vera J, Wolkenhauer O (2008) A system biology approach to understand functional activity of cell communication systems. Methods Cell Biol 90:399-415
    • (2008) Methods Cell Biol , vol.90 , pp. 399-415
    • Vera, J.1    Wolkenhauer, O.2
  • 26
    • 51749122228 scopus 로고    scopus 로고
    • Dynamical modeling and multi-experiment fitting with PottersWheel
    • Maiwald T, Timmer J (2008) Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics 24:2037-2043
    • (2008) Bioinformatics , vol.24 , pp. 2037-2043
    • Maiwald, T.1    Timmer, J.2
  • 29
    • 34547555796 scopus 로고    scopus 로고
    • Global and local architecture of the mammalian microRNAtranscription factor regulatory network
    • Shalgi R, Lieber D, Oren M, Pilpel Y (2007) Global and local architecture of the mammalian microRNAtranscription factor regulatory network. PLoS Comput Biol 3:e131
    • (2007) PLoS Comput Biol , vol.3
    • Shalgi, R.1    Lieber, D.2    Oren, M.3    Pilpel, Y.4
  • 31
    • 84892909562 scopus 로고    scopus 로고
    • Modelling miRNA regulation in cancer signalling systems: MiR-34a regulation of the p53/Sirt1 signalling module
    • Liu X, Betterton M (eds.), Humana press, ISBN: 9781617798230
    • Lai X, Wolkenhauer O, Vera J (2012) Modelling miRNA regulation in cancer signalling systems: miR-34a regulation of the p53/Sirt1 signalling module. In: Computational modelling of signalling networks, Liu X, Betterton M (eds.), Humana press 2012, ISBN: 9781617798230
    • (2012) Computational Modelling of Signalling Networks , vol.2012
    • Lai, X.1    Wolkenhauer, O.2    Vera, J.3
  • 33
    • 35248896405 scopus 로고    scopus 로고
    • Principal difference between stability and structural stability (robustness) as used in systems biology
    • Nikolov S, Yankulova E, Wolkenhauer O, Petrov V (2007) Principal difference between stability and structural stability (robustness) as used in systems biology. Nonlinear Dynamics Psychol Life Sci 11: 413-433
    • (2007) Nonlinear Dynamics Psychol Life Sci , vol.11 , pp. 413-433
    • Nikolov, S.1    Yankulova, E.2    Wolkenhauer, O.3    Petrov, V.4
  • 34
    • 34547607606 scopus 로고    scopus 로고
    • Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations
    • Sorribas A, Hernández-Bermejo B, Vilaprinyo E, Alves R (2007) Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximations. Biotechnol Bioeng 97:1259-1277
    • (2007) Biotechnol Bioeng , vol.97 , pp. 1259-1277
    • Sorribas, A.1    Hernández-Bermejo, B.2    Vilaprinyo, E.3    Alves, R.4
  • 35
    • 34249819336 scopus 로고    scopus 로고
    • MicroRNAmediated feedback and feedforward loops are recurrent network motifs in mammals
    • Tsang J, Zhu J, van Oudenaarden A (2007) MicroRNAmediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26:753-767
    • (2007) Mol Cell , vol.26 , pp. 753-767
    • Tsang, J.1    Zhu, J.2    Van Oudenaarden, A.3
  • 36
    • 79952302623 scopus 로고    scopus 로고
    • The role of incoherent microRNA-mediated feedforward loops in noise buffering
    • Osella M, Bosia C, Corá D, Caselle M (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    Corá, D.3    Caselle, M.4
  • 37
    • 0142027814 scopus 로고    scopus 로고
    • Structure and function of the feed-forward loop network motif
    • Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100:11980-11985
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 11980-11985
    • Mangan, S.1    Alon, U.2
  • 38
    • 70349334678 scopus 로고    scopus 로고
    • Genomewide survey of microRNA-transcription factor feedforward regulatory circuits in human
    • Re A, Corá D, Taverna D, Caselle M (2009) Genomewide survey of microRNA-transcription factor feedforward regulatory circuits in human. Mol Biosyst 5:854-867
    • (2009) Mol Biosyst , vol.5 , pp. 854-867
    • Re, A.1    Corá, D.2    Taverna, D.3    Caselle, M.4
  • 39
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • Doench JG, Sharp PA (2004) Specificity of microRNA target selection in translational repression. Genes Dev 18:504-511
    • (2004) Genes Dev , vol.18 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 41
    • 0027496935 scopus 로고
    • The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases
    • Harper JW, Adami GR, Wei N, Keyomarsi K, Elledge SJ (1993) The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell 75:805-816
    • (1993) Cell , vol.75 , pp. 805-816
    • Harper, J.W.1    Adami, G.R.2    Wei, N.3    Keyomarsi, K.4    Elledge, S.J.5
  • 42
    • 77949795326 scopus 로고    scopus 로고
    • The two stem cell microRNA gene clusters C19MC and miR-371-3 are activated by specific chromosomal rearrangements in a subgroup of thyroid adenomas
    • Rippe V, Dittberner L, Lorenz VN, Drieschner N, Nimzyk R, Sendt W, Junker K, Belge G, Bullerdiek J (2010) The two stem cell microRNA gene clusters C19MC and miR-371-3 are activated by specific chromosomal rearrangements in a subgroup of thyroid adenomas. PLoS One 5:e9485
    • (2010) PLoS One , vol.5
    • Rippe, V.1    Dittberner, L.2    Lorenz, V.N.3    Drieschner, N.4    Nimzyk, R.5    Sendt, W.6    Junker, K.7    Belge, G.8    Bullerdiek, J.9
  • 43
    • 11444251652 scopus 로고    scopus 로고
    • New human and mouse microRNA genes found by homology search
    • Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272:59-73
    • (2005) FEBS J , vol.272 , pp. 59-73
    • Weber, M.J.1
  • 46
    • 0001244976 scopus 로고    scopus 로고
    • Sensitivity analysis as an ingredient of modeling
    • Saltelli A, Tarantola S, Campolongo F (2000) Sensitivity analysis as an ingredient of modeling. Stat Sci 15:377-395
    • (2000) Stat Sci , vol.15 , pp. 377-395
    • Saltelli, A.1    Tarantola, S.2    Campolongo, F.3
  • 47
    • 36849064251 scopus 로고    scopus 로고
    • Targetspecific and global effectors in gene regulation by MicroRNA
    • Levine E, Ben Jacob E, Levine H (2007) Targetspecific and global effectors in gene regulation by MicroRNA. Biophys J 93:L52-L54
    • (2007) Biophys J , vol.93
    • Levine, E.1    Ben Jacob, E.2    Levine, H.3
  • 48
    • 77953629046 scopus 로고    scopus 로고
    • Regulation of mRNA translation and stability by microRNAs
    • Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79:351-379
    • (2010) Annu Rev Biochem , vol.79 , pp. 351-379
    • Fabian, M.R.1    Sonenberg, N.2    Filipowicz, W.3
  • 49
    • 47949097974 scopus 로고    scopus 로고
    • Computational analysis of miRNA-mediated repression of translation: Implications for models of translation initiation inhibition
    • Nissan T, Parker R (2008) Computational analysis of miRNA-mediated repression of translation: implications for models of translation initiation inhibition. RNA 14:1480-1491
    • (2008) RNA , vol.14 , pp. 1480-1491
    • Nissan, T.1    Parker, R.2
  • 53
    • 42049105840 scopus 로고    scopus 로고
    • Dissecting microregulation of a master regulatory network
    • Sinha AU, Kaimal V, Chen J, Jegga AG (2008) Dissecting microregulation of a master regulatory network. BMC Genomics 9:88
    • (2008) BMC Genomics , vol.9 , pp. 88
    • Sinha, A.U.1    Kaimal, V.2    Chen, J.3    Jegga, A.G.4
  • 54
    • 65449151411 scopus 로고    scopus 로고
    • The interplay between transcription factors and microRNAs in genome-scale regulatory networks
    • Martinez NJ, Walhout AJM (2009) The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays 31:435-445
    • (2009) Bioessays , vol.31 , pp. 435-445
    • Martinez, N.J.1    Walhout, A.J.M.2
  • 55
    • 71949106691 scopus 로고    scopus 로고
    • Dynamics of microRNA-mediated motifs
    • Xu F, Liu Z, Shen J, Wang R (2009) Dynamics of microRNA-mediated motifs. IET Syst Biol 3:496-504
    • (2009) IET Syst Biol , vol.3 , pp. 496-504
    • Xu, F.1    Liu, Z.2    Shen, J.3    Wang, R.4
  • 56
    • 34249006516 scopus 로고    scopus 로고
    • The role of microRNA in the delayed negative feedback regulation of gene expression
    • Xie Z-R, Yang H-T, Liu W-C, Hwang M-J (2007) The role of microRNA in the delayed negative feedback regulation of gene expression. Biochem Biophys Res Commun 358:722-726
    • (2007) Biochem Biophys Res Commun , vol.358 , pp. 722-726
    • Xie, Z.-R.1    Yang, H.-T.2    Liu, W.-C.3    Hwang, M.-J.4
  • 59
    • 33748587841 scopus 로고    scopus 로고
    • A patternbased method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    • Miranda KC, Huynh T, Tay Y, Ang Y-S, Tam W-L, Thomson AM, Lim B, Rigoutsos I (2006) A patternbased method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 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
  • 60
    • 43049133807 scopus 로고    scopus 로고
    • MicroRNA let-7b targets important cell cycle molecules in malignant melanoma cells and interferes with anchorage-independent growth
    • Schultz J, Lorenz P, Gross G, Ibrahim S, Kunz M (2008) MicroRNA let-7b targets important cell cycle molecules in malignant melanoma cells and interferes with anchorage-independent growth. Cell Res 18:549-557
    • (2008) Cell Res , vol.18 , pp. 549-557
    • Schultz, J.1    Lorenz, P.2    Gross, G.3    Ibrahim, S.4    Kunz, M.5
  • 63
    • 33646444884 scopus 로고    scopus 로고
    • Let-7 microRNA functions as a potential growth suppressor in human colon cancer cells
    • Akao Y, Nakagawa Y, Naoe T (2006) let-7 microRNA functions as a potential growth suppressor in human colon cancer cells. Biol Pharm Bull 29:903-906
    • (2006) Biol Pharm Bull , vol.29 , pp. 903-906
    • Akao, Y.1    Nakagawa, Y.2    Naoe, T.3
  • 65
    • 22244467087 scopus 로고    scopus 로고
    • MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells
    • Chan JA, Krichevsky AM, Kosik KS (2005) MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 65:6029-6033
    • (2005) Cancer Res , vol.65 , pp. 6029-6033
    • Chan, J.A.1    Krichevsky, A.M.2    Kosik, K.S.3
  • 66
    • 41349120349 scopus 로고    scopus 로고
    • Computational modeling of post-transcriptional gene regulation by microRNAs
    • Khanin R, Vinciotti V (2008) Computational modeling of post-transcriptional gene regulation by microRNAs. J Comput Biol 15:305-316
    • (2008) J Comput Biol , vol.15 , pp. 305-316
    • Khanin, R.1    Vinciotti, V.2
  • 68
    • 77952299722 scopus 로고    scopus 로고
    • MiR-124 and miR-203 are epigenetically silenced tumour-suppressive microRNAs in hepatocellular carcinoma
    • Furuta M, Kozaki K, Tanaka S, Arii S, Imoto I, Inazawa J (2010) miR-124 and miR-203 are epigenetically silenced tumour-suppressive microRNAs in hepatocellular carcinoma. Carcinogenesis 31:766-776
    • (2010) Carcinogenesis , vol.31 , pp. 766-776
    • Furuta, M.1    Kozaki, K.2    Tanaka, S.3    Arii, S.4    Imoto, I.5    Inazawa, J.6
  • 70
    • 77955840320 scopus 로고    scopus 로고
    • Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation
    • Vohradsky J, Panek J, 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.