메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis

Author keywords

Competing endogeneous RNA; MicroRNA network; MicroRNA target bicluster

Indexed keywords

COMPETING ENDOGENOUS RNA; MESSENGER RNA; MICRORNA; RNA; UNCLASSIFIED DRUG;

EID: 84964312596     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1178     Document Type: Article
Times cited : (10)

References (77)
  • 1
    • 0036828639 scopus 로고    scopus 로고
    • The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis
    • Carmell MA, Xuan Z, Zhang MQ, Hannon GJ: The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 2002, 16(21):2733-2742.
    • (2002) Genes Dev , vol.16 , Issue.21 , pp. 2733-2742
    • Carmell, M.A.1    Xuan, Z.2    Zhang, M.Q.3    Hannon, G.J.4
  • 2
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis,mechanism, and function
    • Bartel DP: MicroRNAs: Genomics, biogenesis,mechanism, and function. Cell 2004, 116(2):281-297.
    • (2004) Cell , vol.116 , Issue.2 , pp. 281-297
    • Bartel, D.P.1
  • 3
    • 33644768174 scopus 로고    scopus 로고
    • Control of translation andmRNA degradation by miRNAs and siRNAs
    • Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R: Control of translation andmRNA degradation by miRNAs and siRNAs. Genes Dev 2006, 20(5):515-524.
    • (2006) Genes Dev , vol.20 , Issue.5 , pp. 515-524
    • Valencia-Sanchez, M.A.1    Liu, J.2    Hannon, G.J.3    Parker, R.4
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 8
    • 79961170994 scopus 로고    scopus 로고
    • A ceRNA Hypothesis: the Rosetta stone of a hidden RNA language?
    • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP: A ceRNA Hypothesis: the Rosetta stone of a hidden RNA language? Cell 2011, 146:353-358.
    • (2011) Cell , vol.146 , pp. 353-358
    • Salmena, L.1    Poliseno, L.2    Tay, Y.3    Kats, L.4    Pandolfi, P.P.5
  • 10
    • 84860324470 scopus 로고    scopus 로고
    • Roles for MicroRNAs in conferring robustness to biological processes
    • Ebert MS, Sharp PA: Roles for MicroRNAs in conferring robustness to biological processes. Cell 2012, 149:515-524.
    • (2012) Cell , vol.149 , pp. 515-524
    • Ebert, M.S.1    Sharp, P.A.2
  • 11
    • 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, Havenman WJ, Pandolfi PP: A coding-independent function of gene and Pseudogene mRNAs regulates tumour biology. Nature 2010, 465(7301):1033-1038.
    • (2010) Nature , vol.465 , Issue.7301 , pp. 1033-1038
    • Poliseno, L.1    Salmena, L.2    Zhang, J.3    Carver, B.4    Havenman, W.J.5    Pandolfi, P.P.6
  • 17
    • 34249849395 scopus 로고    scopus 로고
    • Discovery of microRNA-mRNAmodules via population-based probabilistic learning
    • Joung JG, Hwang KB, Nam JW, Kim SJ, Zhang BT: Discovery of microRNA-mRNAmodules via population-based probabilistic learning. Bioinformatics 2007, 23(9):1141-1147.
    • (2007) Bioinformatics , vol.23 , Issue.9 , pp. 1141-1147
    • Joung, J.G.1    Hwang, K.B.2    Nam, J.W.3    Kim, S.J.4    Zhang, B.T.5
  • 18
    • 57649228450 scopus 로고    scopus 로고
    • Finding MicroRNA regulatory modules in human genome using rule induction
    • Tran DH, Satou K, Ho TB: Finding MicroRNA regulatory modules in human genome using rule induction. BMC Bioinformatics 2008, 9(S5).
    • (2008) BMC Bioinformatics , vol.9
    • Tran, D.H.1    Satou, K.2    Ho, T.B.3
  • 20
    • 74049088856 scopus 로고    scopus 로고
    • Lost in translation: an assessment and perspective for computationalmicroRNA target identification
    • Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG: Lost in translation: an assessment and perspective for computationalmicroRNA target identification. Bioinformatics 2009, 25(23):3049-3055.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3049-3055
    • Alexiou, P.1    Maragkakis, M.2    Papadopoulos, G.L.3    Reczko, M.4    Hatzigeorgiou, A.G.5
  • 24
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 28
    • 67649382719 scopus 로고    scopus 로고
    • Discovery of functionalmiRNA-mRNA regulatory modules with computational methods
    • Liu B, Li J, Tsykin A: Discovery of functionalmiRNA-mRNA regulatory modules with computational methods. J Biomed Inform 2009, 42:685-691.
    • (2009) J Biomed Inform , vol.42 , pp. 685-691
    • Liu, B.1    Li, J.2    Tsykin, A.3
  • 30
    • 77953312769 scopus 로고    scopus 로고
    • Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals alteredmiRNA regulation
    • Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ: Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals alteredmiRNA regulation. PLOS ONE 2010, 5(e8898).
    • (2010) PLOS ONE , vol.5
    • Nunez-Iglesias, J.1    Liu, C.C.2    Morgan, T.E.3    Finch, C.E.4    Zhou, X.J.5
  • 31
    • 75349100888 scopus 로고    scopus 로고
    • mimiRNA: amicroRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets
    • Ritchie W, Flamant S, Rasko JEJ: mimiRNA: amicroRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics 2010, 26(2):223-227.
    • (2010) Bioinformatics , vol.26 , Issue.2 , pp. 223-227
    • Ritchie, W.1    Flamant, S.2    Rasko, J.E.J.3
  • 32
    • 80051931399 scopus 로고    scopus 로고
    • A Lasso regression model for the construction ofmicroRNA-target regulatory networks
    • Lu Y, Zhou Y, Qu W, Deng M, Zhang C: A Lasso regression model for the construction ofmicroRNA-target regulatory networks. Bioinformatics 2011, 27(17):2406-2413.
    • (2011) Bioinformatics , vol.27 , Issue.17 , pp. 2406-2413
    • Lu, Y.1    Zhou, Y.2    Qu, W.3    Deng, M.4    Zhang, C.5
  • 34
    • 39849111033 scopus 로고    scopus 로고
    • miRNAminer: A tool for homologous microRNA gene search
    • Artzi S, Kiezun A, Shomron N: miRNAminer: A tool for homologous microRNA gene search. BMC Bioinformatics 2008, 9:39.
    • (2008) BMC Bioinformatics , vol.9 , pp. 39
    • Artzi, S.1    Kiezun, A.2    Shomron, N.3
  • 36
    • 80052339890 scopus 로고    scopus 로고
    • From structure prediction to genomic screens for novel non-coding RNAs
    • Gorodkin J, Hofacker IL: From structure prediction to genomic screens for novel non-coding RNAs. PLoS Comput Biol 2011, 7(8):e1002100.
    • (2011) PLoS Comput Biol , vol.7 , Issue.8
    • Gorodkin, J.1    Hofacker, I.L.2
  • 37
    • 77951953262 scopus 로고    scopus 로고
    • Got Target?: computationalmethods formicroRNA target prediction and their extension
    • Min H, Yoon S: Got Target?: computationalmethods formicroRNA target prediction and their extension. Exp MolMed 2010, 42(4):233-244.
    • (2010) Exp MolMed , vol.42 , Issue.4 , pp. 233-244
    • Min, H.1    Yoon, S.2
  • 38
    • 77957766910 scopus 로고    scopus 로고
    • Desperately seekingmicroRNA targets
    • Thomas M, Lieberman J, Lal A: Desperately seekingmicroRNA targets. Nat Struct Mol Biol 2010, 17(10):1169-1174.
    • (2010) Nat Struct Mol Biol , vol.17 , Issue.10 , pp. 1169-1174
    • Thomas, M.1    Lieberman, J.2    Lal, A.3
  • 39
    • 59549088112 scopus 로고    scopus 로고
    • Identification of MicroRNA regulatory modules in arabidopsis via a probabilistic graphical model
    • Joung JG, Fei Z: Identification of MicroRNA regulatory modules in arabidopsis via a probabilistic graphical model. Bioinformatics 2009, 25(3):387-393.
    • (2009) Bioinformatics , vol.25 , Issue.3 , pp. 387-393
    • Joung, J.G.1    Fei, Z.2
  • 40
    • 73249118535 scopus 로고    scopus 로고
    • Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy
    • Liu B, Li J, Tsykin A, Liu L, Gaur AB, Goodall GJ: Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy. BMC Bioinformatics 2009, 10(408).
    • (2009) BMC Bioinformatics , vol.10 , Issue.408
    • Liu, B.1    Li, J.2    Tsykin, A.3    Liu, L.4    Gaur, A.B.5    Goodall, G.J.6
  • 41
    • 77956308091 scopus 로고    scopus 로고
    • Module network inference from a cancer gene expression data set identifiesmicroRNA regulatedmodules
    • Bonnet E, Tatari M, Joshi A, Michoel T, Marchal K, Berx G, de Peer YV: Module network inference from a cancer gene expression data set identifiesmicroRNA regulatedmodules. PLOS ONE 2010, 5:e10162.
    • (2010) PLOS ONE , vol.5
    • Bonnet, E.1    Tatari, M.2    Joshi, A.3    Michoel, T.4    Marchal, K.5    Berx, G.6    de Peer, Y.V.7
  • 42
    • 79951751828 scopus 로고    scopus 로고
    • Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation
    • Liu B, Liu L, Tsykin A, Goodall GJ, Green JE, Zhu M, Kim CH, Li J: Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation. Bioinformatics 2010, 26(24):3105-3111.
    • (2010) Bioinformatics , vol.26 , Issue.24 , pp. 3105-3111
    • Liu, B.1    Liu, L.2    Tsykin, A.3    Goodall, G.J.4    Green, J.E.5    Zhu, M.6    Kim, C.H.7    Li, J.8
  • 43
    • 79959448071 scopus 로고    scopus 로고
    • A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules
    • Zhang S, Li Q, Liu J, Zhou XJ: A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics 2011, 27:i401-i409.
    • (2011) Bioinformatics , vol.27 , pp. i401-i409
    • Zhang, S.1    Li, Q.2    Liu, J.3    Zhou, X.J.4
  • 44
    • 84893025641 scopus 로고    scopus 로고
    • IdentifyingmiRNAs, targets and functions
    • Liu B, Li J, Cairns MJ: IdentifyingmiRNAs, targets and functions. Brief Bioinformatics 2014, 15(1):1-19.
    • (2014) Brief Bioinformatics , vol.15 , Issue.1 , pp. 1-19
    • Liu, B.1    Li, J.2    Cairns, M.J.3
  • 45
    • 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
  • 46
    • 27544458484 scopus 로고    scopus 로고
    • Prediction of regulatory modules comprising microRNAs and target genes
    • Yoon S, De Micheli G: Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 2005, 21(Suppl. 2):ii93-ii100.
    • (2005) Bioinformatics , vol.21 , pp. ii93-ii100
    • Yoon, S.1    De Micheli, G.2
  • 48
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008, 4:44-57.
    • (2008) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 49
    • 84879887496 scopus 로고    scopus 로고
    • MiR-320a is Downregulated in patients with myasthenia gravis andmodulates inflammatory Cytokines production by targeting mitogen-activated protein kinase 1
    • Cheng Z, Qiu S, Jiang L, Zhang A, Bao W, Liu P, Liu J: MiR-320a is Downregulated in patients with myasthenia gravis andmodulates inflammatory Cytokines production by targeting mitogen-activated protein kinase 1. J Clin Immunol 2013, 33:567-576.
    • (2013) J Clin Immunol , vol.33 , pp. 567-576
    • Cheng, Z.1    Qiu, S.2    Jiang, L.3    Zhang, A.4    Bao, W.5    Liu, P.6    Liu, J.7
  • 51
    • 84866723283 scopus 로고    scopus 로고
    • The miR-17 family links p63 protein to MAPK signaling to promote the onset of human keratinocyte differentiation
    • Wu N, Sulpice E, Obeid P, Benzina S, Kermarrec F, Combe S, Gidrol X: The miR-17 family links p63 protein to MAPK signaling to promote the onset of human keratinocyte differentiation. PLOS ONE 2012, 7(e45761).
    • (2012) PLOS ONE , vol.7
    • Wu, N.1    Sulpice, E.2    Obeid, P.3    Benzina, S.4    Kermarrec, F.5    Combe, S.6    Gidrol, X.7
  • 53
    • 34247565615 scopus 로고    scopus 로고
    • The tumor suppressormicroRNA let-7 represses the HMGA2 oncogene
    • Lee YS, Dutta A: The tumor suppressormicroRNA let-7 represses the HMGA2 oncogene. Genes Dev 2007, 21(9):1025-1030.
    • (2007) Genes Dev , vol.21 , Issue.9 , pp. 1025-1030
    • Lee, Y.S.1    Dutta, A.2
  • 54
    • 33947431322 scopus 로고    scopus 로고
    • Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation
    • Mayr C, Hemann MT, Bartel DP: Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 2008, 315(5818):1576-1579.
    • (2008) Science , vol.315 , Issue.5818 , pp. 1576-1579
    • Mayr, C.1    Hemann, M.T.2    Bartel, D.P.3
  • 56
    • 84857784512 scopus 로고    scopus 로고
    • Senescence is an endogenous trigger for MicroRNA-directed transcriptional gene silencing in human cells
    • Benhamed M, Herbig U, Ye T, Dejean A, Bischof O: Senescence is an endogenous trigger for MicroRNA-directed transcriptional gene silencing in human cells. Nat Cell Biol 2012, 14(3):266-275.
    • (2012) Nat Cell Biol , vol.14 , Issue.3 , pp. 266-275
    • Benhamed, M.1    Herbig, U.2    Ye, T.3    Dejean, A.4    Bischof, O.5
  • 57
    • 42049092138 scopus 로고    scopus 로고
    • Downregulation of CCND1 and CDK6 bymiR-34a induces cell cycle arrest
    • Sun F, Fu H, Liu Q, Tie Y, Zhu J, Xing R, Sun Z, Zheng X: Downregulation of CCND1 and CDK6 bymiR-34a induces cell cycle arrest. FEBS Lett 2008, 582:1564-1568.
    • (2008) FEBS Lett , vol.582 , pp. 1564-1568
    • Sun, F.1    Fu, H.2    Liu, Q.3    Tie, Y.4    Zhu, J.5    Xing, R.6    Sun, Z.7    Zheng, X.8
  • 61
    • 84896270599 scopus 로고    scopus 로고
    • Tumor suppressor microRNA-34a inhibits cell proliferation by targeting Notch1 in renal cell carcinoma
    • Zhang C, Mo R, Yin B, Zhou L, Liu Y, Fan J: Tumor suppressor microRNA-34a inhibits cell proliferation by targeting Notch1 in renal cell carcinoma. Oncol Lett 2014, 7(5):1689-1694.
    • (2014) Oncol Lett , vol.7 , Issue.5 , pp. 1689-1694
    • Zhang, C.1    Mo, R.2    Yin, B.3    Zhou, L.4    Liu, Y.5    Fan, J.6
  • 66
    • 84878187639 scopus 로고    scopus 로고
    • MicroRNA-106b-25 cluster targets β-TRCP2, increases the expression of snail and enhances cell migration and invasion in H1299 (non small cell lung cancer) cells
    • Savita U, Karunagaran D: MicroRNA-106b-25 cluster targets β-TRCP2, increases the expression of snail and enhances cell migration and invasion in H1299 (non small cell lung cancer) cells. Bioch Biophys Res Commun 2013, 434:841-847.
    • (2013) Bioch Biophys Res Commun , vol.434 , pp. 841-847
    • Savita, U.1    Karunagaran, D.2
  • 67
    • 84875196536 scopus 로고    scopus 로고
    • COXPRESdb: A database of comparative gene Coexpression networks of eleven species formammals
    • Obayashi T, Okamura Y, Ito S, Tadaka S, Motoike IN, Kinoshita K: COXPRESdb: A database of comparative gene Coexpression networks of eleven species formammals. Nucleic Acids Res 2013, 41:D1014-D1020.
    • (2013) Nucleic Acids Res , vol.41 , pp. D1014-D1020
    • Obayashi, T.1    Okamura, Y.2    Ito, S.3    Tadaka, S.4    Motoike, I.N.5    Kinoshita, K.6
  • 70
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E: The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39(10):1278-1284.
    • (2007) Nat Genet , vol.39 , Issue.10 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 71
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 73
    • 0141998079 scopus 로고    scopus 로고
    • Themaximum edge Biclique problem is NP-complete
    • Peeters R: Themaximum edge Biclique problem is NP-complete. Discrete Appl Math 2003, 131(3):651-654.
    • (2003) Discrete Appl Math , vol.131 , Issue.3 , pp. 651-654
    • Peeters, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.