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Volumn 7, Issue 12, 2011, Pages

A densely interconnected genome-wide network of micrornas and oncogenic pathways revealed using gene expression signatures

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON; MICRORNA; MYC PROTEIN; PROTEIN P53; STAT PROTEIN; WNT PROTEIN; CARCINOGEN; MESSENGER RNA;

EID: 84855262919     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002415     Document Type: Article
Times cited : (26)

References (45)
  • 1
    • 33748928159 scopus 로고    scopus 로고
    • The diverse functions of microRNAs in animal development and disease
    • Kloosterman WP, Plasterk RH, (2006) The diverse functions of microRNAs in animal development and disease. Developmental Cell 11: 441-450.
    • (2006) Developmental Cell , vol.11 , pp. 441-450
    • Kloosterman, W.P.1    Plasterk, R.H.2
  • 2
    • 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
  • 3
    • 54249158400 scopus 로고    scopus 로고
    • Emerging Role of miR-106b-25/miR-17-92 Clusters in the Control of Transforming Growth Factor β Signaling
    • Petrocca F, Vecchione A, Croce CM, (2008) Emerging Role of miR-106b-25/miR-17-92 Clusters in the Control of Transforming Growth Factor β Signaling. Cancer Research 68: 8191-8191.
    • (2008) Cancer Research , vol.68 , pp. 8191
    • Petrocca, F.1    Vecchione, A.2    Croce, C.M.3
  • 4
    • 37549008310 scopus 로고    scopus 로고
    • Widespread microRNA repression by Myc contributes to tumorigenesis
    • Chang TC, Yu D, Lee YS, Wentzel EA, Arking DE, et al. (2008) Widespread microRNA repression by Myc contributes to tumorigenesis. Nat Genet 40: 43-50.
    • (2008) Nat Genet , vol.40 , pp. 43-50
    • Chang, T.C.1    Yu, D.2    Lee, Y.S.3    Wentzel, E.A.4    Arking, D.E.5
  • 6
    • 78649743127 scopus 로고    scopus 로고
    • Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs
    • Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, et al. (2010) Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood 116: e118-127.
    • (2010) Blood , vol.116
    • Jima, D.D.1    Zhang, J.2    Jacobs, C.3    Richards, K.L.4    Dunphy, C.H.5
  • 7
    • 77950348609 scopus 로고    scopus 로고
    • Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures
    • Tsang J, Ebert M, van Oudenaarden A, (2010) Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell 38: 140-153.
    • (2010) Mol Cell , vol.38 , pp. 140-153
    • Tsang, J.1    Ebert, M.2    van Oudenaarden, A.3
  • 9
    • 44149083586 scopus 로고    scopus 로고
    • miRDB: a microRNA target prediction and functional annotation database with a wiki interface
    • Wang X, (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14: 1012-1017.
    • (2008) RNA , vol.14 , pp. 1012-1017
    • Wang, X.1
  • 10
    • 70450172473 scopus 로고    scopus 로고
    • Survey of Computational Algorithms for MicroRNA Target Prediction
    • Yue D, Liu H, Huang Y, (2009) Survey of Computational Algorithms for MicroRNA Target Prediction. Curr Genomics 10: 478-492.
    • (2009) Curr Genomics , vol.10 , pp. 478-492
    • Yue, D.1    Liu, H.2    Huang, Y.3
  • 11
    • 73449130242 scopus 로고    scopus 로고
    • Oncogenic pathway combinations predict clinical prognosis in gastric cancer
    • doi: 10.1371/journal.pgen.1000676
    • Ooi CH, Ivanova T, Wu J, Lee M, Tan IB, et al. (2009) Oncogenic pathway combinations predict clinical prognosis in gastric cancer. PLoS Genet 5: e1000676 doi:10.1371/journal.pgen.1000676.
    • (2009) PLoS Genet , vol.5
    • Ooi, C.H.1    Ivanova, T.2    Wu, J.3    Lee, M.4    Tan, I.B.5
  • 12
    • 26444546442 scopus 로고    scopus 로고
    • An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    • Miller LD, Smeds J, George J, Vega VB, Vergara L, et al. (2005) An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A 102: 13550-13555.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13550-13555
    • Miller, L.D.1    Smeds, J.2    George, J.3    Vega, V.B.4    Vergara, L.5
  • 13
    • 77954038330 scopus 로고    scopus 로고
    • A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors
    • Loboda A, Nebozhyn M, Klinghoffer R, Frazier J, Chastain M, et al. (2010) A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors. BMC Med Genomics 3: 26.
    • (2010) BMC Med Genomics , vol.3 , pp. 26
    • Loboda, A.1    Nebozhyn, M.2    Klinghoffer, R.3    Frazier, J.4    Chastain, M.5
  • 14
    • 31144459985 scopus 로고    scopus 로고
    • Oncogenic pathway signatures in human cancers as a guide to targeted therapies
    • Bild AH, Yao G, Chang JT, Wang Q, Potti A, et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439: 353-357.
    • (2006) Nature , vol.439 , pp. 353-357
    • Bild, A.H.1    Yao, G.2    Chang, J.T.3    Wang, Q.4    Potti, A.5
  • 15
    • 33644872577 scopus 로고    scopus 로고
    • Limma: linear models for microarray data
    • In: R. Gentleman VC, Dudoit S, Irizarry R, Huber W, editors, New York, Springer
    • Smyth GK, (2005) Limma: linear models for microarray data. In: R. Gentleman VC, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and Computational Biology Solutions using R and Bioconductor New York Springer pp. 397-420.
    • (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 17
    • 77954314233 scopus 로고    scopus 로고
    • miR-146a in PBMCs modulates Th1 function in patients with acute coronary syndrome
    • doi: 10.1038/icb.2010.16
    • Guo M, Mao X, Ji Q, Lang M, Li S, et al. (2010) miR-146a in PBMCs modulates Th1 function in patients with acute coronary syndrome. Immunology and Cell Biology doi:10.1038/icb.2010.16.
    • (2010) Immunology and Cell Biology
    • Guo, M.1    Mao, X.2    Ji, Q.3    Lang, M.4    Li, S.5
  • 18
    • 77950467511 scopus 로고    scopus 로고
    • MicroRNA expression in human airway smooth muscle cells: role of miR-25 in regulation of airway smooth muscle phenotype
    • Kuhn A, Schlauch K, Lao R, Halayko A, Gerthoffer WT, et al. (2010) MicroRNA expression in human airway smooth muscle cells: role of miR-25 in regulation of airway smooth muscle phenotype. Am J Respir Cell Mol Biol 42: 506-513.
    • (2010) Am J Respir Cell Mol Biol , vol.42 , pp. 506-513
    • Kuhn, A.1    Schlauch, K.2    Lao, R.3    Halayko, A.4    Gerthoffer, W.T.5
  • 19
    • 59849087052 scopus 로고    scopus 로고
    • MicroRNA-146a modulates human bronchial epithelial cell survival in response to the cytokine-induced apoptosis
    • Liu X, Nelson A, Wang X, Kanaji N, Kim M, et al. (2009) MicroRNA-146a modulates human bronchial epithelial cell survival in response to the cytokine-induced apoptosis. Biochem Biophys Res Commun 380: 177-182.
    • (2009) Biochem Biophys Res Commun , vol.380 , pp. 177-182
    • Liu, X.1    Nelson, A.2    Wang, X.3    Kanaji, N.4    Kim, M.5
  • 20
    • 33747608638 scopus 로고    scopus 로고
    • NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses
    • Taganov KD, Boldin MP, Chang KJ, Baltimore D, (2006) NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A 103: 12481-12486.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 12481-12486
    • Taganov, K.D.1    Boldin, M.P.2    Chang, K.J.3    Baltimore, D.4
  • 21
    • 33646338489 scopus 로고    scopus 로고
    • Epstein-Barr virus infection alters cellular signal cascades in human nasopharyngeal epithelial cells
    • Lo AK, Lo KW, Tsao SW, Wong HL, Hui JW, et al. (2006) Epstein-Barr virus infection alters cellular signal cascades in human nasopharyngeal epithelial cells. Neoplasia 8: 173-180.
    • (2006) Neoplasia , vol.8 , pp. 173-180
    • Lo, A.K.1    Lo, K.W.2    Tsao, S.W.3    Wong, H.L.4    Hui, J.W.5
  • 22
    • 34250868124 scopus 로고    scopus 로고
    • Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest
    • Tarasov V, Jung P, Verdoodt B, Lodygin D, Epanchintsev A, et al. (2007) Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest. Cell Cycle 6: 1586-1593.
    • (2007) Cell Cycle , vol.6 , pp. 1586-1593
    • Tarasov, V.1    Jung, P.2    Verdoodt, B.3    Lodygin, D.4    Epanchintsev, A.5
  • 23
    • 70349220767 scopus 로고    scopus 로고
    • Repression of the miR-17-92 cluster by p53 has an important function in hypoxia-induced apoptosis
    • Yan HL, Xue G, Mei Q, Wang YZ, Ding FX, et al. (2009) Repression of the miR-17-92 cluster by p53 has an important function in hypoxia-induced apoptosis. EMBO J 28: 2719-2732.
    • (2009) EMBO J , vol.28 , pp. 2719-2732
    • Yan, H.L.1    Xue, G.2    Mei, Q.3    Wang, Y.Z.4    Ding, F.X.5
  • 24
    • 77956942286 scopus 로고    scopus 로고
    • WLS-dependent secretion of WNT3A requires Ser209 acylation and vacuolar acidification
    • Coombs GS, Yu J, Canning CA, Veltri CA, Covey TM, et al. (2010) WLS-dependent secretion of WNT3A requires Ser209 acylation and vacuolar acidification. J Cell Sci 123: 3357-3367.
    • (2010) J Cell Sci , vol.123 , pp. 3357-3367
    • Coombs, G.S.1    Yu, J.2    Canning, C.A.3    Veltri, C.A.4    Covey, T.M.5
  • 25
    • 0030975671 scopus 로고    scopus 로고
    • Constitutive transcriptional activation by a β-catenin -Tcf complex in APC-/- colon carcinoma
    • Korinek V, Barker N, Morin PJ, van Wichen D, de Weger R, et al. (1997) Constitutive transcriptional activation by a β-catenin-Tcf complex in APC-/- colon carcinoma. Science 275: 1784-1787.
    • (1997) Science , vol.275 , pp. 1784-1787
    • Korinek, V.1    Barker, N.2    Morin, P.J.3    van Wichen, D.4    de Weger, R.5
  • 26
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102 (43): 15545-15550.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.43 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5
  • 27
    • 13144286421 scopus 로고    scopus 로고
    • Receptor and secreted targets of Wnt-1/β-catenin signalling in mouse mammary epithelial cells
    • Kenny PA, Enver T, Ashworth A, (2005) Receptor and secreted targets of Wnt-1/β-catenin signalling in mouse mammary epithelial cells. BMC Cancer 5: 3.
    • (2005) BMC Cancer , vol.5 , pp. 3
    • Kenny, P.A.1    Enver, T.2    Ashworth, A.3
  • 28
    • 0035418568 scopus 로고    scopus 로고
    • Identification of AF17 as a downstream gene of the β-catenin T-cell factor pathway and its involvement in colorectal carcinogenesis
    • Lin YM, Ono K, Satoh S, Ishiguro H, Fujita M, et al. (2001) Identification of AF17 as a downstream gene of the β-catenin T-cell factor pathway and its involvement in colorectal carcinogenesis. Cancer Research 61: 6345-6349.
    • (2001) Cancer Research , vol.61 , pp. 6345-6349
    • Lin, Y.M.1    Ono, K.2    Satoh, S.3    Ishiguro, H.4    Fujita, M.5
  • 29
    • 3042514191 scopus 로고    scopus 로고
    • Coexpression analysis of human genes across many microarray data sets
    • Lee H, Hsu A, Sajdak J, Qin J, Pavlidis P, (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res 14: 1085-1094.
    • (2004) Genome Res , vol.14 , pp. 1085-1094
    • Lee, H.1    Hsu, A.2    Sajdak, J.3    Qin, J.4    Pavlidis, P.5
  • 30
    • 18044377963 scopus 로고    scopus 로고
    • Principles of MicroRNA-Target Recognition
    • doi: 10.1371/journal.pbio.0030085
    • Brennecke J, Stark A, Russell RB, Cohen SM, (2005) Principles of MicroRNA-Target Recognition. PLoS Biol 3: e85 doi:10.1371/journal.pbio.0030085.
    • (2005) PLoS Biol , vol.3
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3    Cohen, S.M.4
  • 33
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts DJ, Strogatz SH, (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 34
    • 0036353494 scopus 로고    scopus 로고
    • Small world patterns in food webs
    • Montoya JM, Sol RV, (2002) Small world patterns in food webs. J Theor Biol 214: 405-412.
    • (2002) J Theor Biol , vol.214 , pp. 405-412
    • Montoya, J.M.1    Sol, R.V.2
  • 35
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nature Review Genetics 5: 101-113.
    • (2004) Nature Review Genetics , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 36
    • 4644292576 scopus 로고    scopus 로고
    • The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
    • van Noort V, Snel B, Huynen MA, (2004) The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Reports 5: 280-284.
    • (2004) EMBO Reports , vol.5 , pp. 280-284
    • van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 37
    • 33749335282 scopus 로고    scopus 로고
    • The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
    • Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313 (5795): 1929-1935.
    • (2006) Science , vol.313 , Issue.5795 , pp. 1929-1935
    • Lamb, J.1    Crawford, E.D.2    Peck, D.3    Modell, J.W.4    Blat, I.C.5
  • 39
    • 36349035211 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155
    • Skalsky RL, Samols MA, Plaisance KB, Boss IW, Riva A, et al. (2007) Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol 81: 12836-12845.
    • (2007) J Virol , vol.81 , pp. 12836-12845
    • Skalsky, R.L.1    Samols, M.A.2    Plaisance, K.B.3    Boss, I.W.4    Riva, A.5
  • 41
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genome-wide experiments
    • Storey JD, Tibshirani R, (2003) Statistical significance for genome-wide experiments. Proc Natl Acad Sci U S A 100: 9440-9445.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 42
    • 49249097447 scopus 로고    scopus 로고
    • Inhibition of Gastric Cancer Invasion and Metastasis by PLA2G2A, a Novel β-catenin/TCF Target Gene
    • Ganesan K, Ivanova T, Wu Y, Rajasegaran V, Wu J, et al. (2008) Inhibition of Gastric Cancer Invasion and Metastasis by PLA2G2A, a Novel β-catenin/TCF Target Gene. Cancer Res 68: 4277-4286.
    • (2008) Cancer Res , vol.68 , pp. 4277-4286
    • Ganesan, K.1    Ivanova, T.2    Wu, Y.3    Rajasegaran, V.4    Wu, J.5
  • 43
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson WE, Li C, Rabinovic A, (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118-127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 44
    • 0003736078 scopus 로고    scopus 로고
    • Introduction to Graph Theory: Prentice Hall
    • West DB, (2001) Introduction to Graph Theory: Prentice Hall.
    • (2001)
    • West, D.B.1


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