메뉴 건너뛰기




Volumn 9, Issue 5, 2014, Pages

Identification of miRNA-mediated core gene module for glioma patient prediction by integrating high-throughput miRNA, mRNA expression and pathway structure

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

EID: 84901049591     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096908     Document Type: Article
Times cited : (28)

References (51)
  • 3
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 4
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • DOI 10.1038/nrg1379
    • He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531. (Pubitemid 38868508)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.7 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 5
    • 77955518808 scopus 로고    scopus 로고
    • Integrated miRNA and mRNA expression profiling of the inflammatory breast cancer subtype
    • Van der Auwera I, Limame R, van Dam P, Vermeulen PB, Dirix LY, et al. (2010) Integrated miRNA and mRNA expression profiling of the inflammatory breast cancer subtype. Br J Cancer 103: 532-541.
    • (2010) Br J Cancer , vol.103 , pp. 532-541
    • Van Der Auwera, I.1    Limame, R.2    Van Dam, P.3    Vermeulen, P.B.4    Dirix, L.Y.5
  • 6
    • 80051643110 scopus 로고    scopus 로고
    • Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage
    • Zhu M, Yi M, Kim CH, Deng C, Li Y, et al. (2011) Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage. Genome Biol 12: R77.
    • (2011) Genome Biol , vol.12
    • Zhu, M.1    Yi, M.2    Kim, C.H.3    Deng, C.4    Li, Y.5
  • 7
    • 78649647583 scopus 로고    scopus 로고
    • Investigation gene and microRNA expression in glioblastoma
    • Dong H, Siu H, Luo L, Fang X, Jin L, et al. (2010) Investigation gene and microRNA expression in glioblastoma. BMC Genomics 11 Suppl 3: S16.
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 3
    • Dong, H.1    Siu, H.2    Luo, L.3    Fang, X.4    Jin, L.5
  • 8
    • 78649348286 scopus 로고    scopus 로고
    • Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma
    • Dong H, Luo L, Hong S, Siu H, Xiao Y, et al. (2010) Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma. BMC Syst Biol 4: 163.
    • (2010) BMC Syst Biol , vol.4 , pp. 163
    • Dong, H.1    Luo, L.2    Hong, S.3    Siu, H.4    Xiao, Y.5
  • 9
    • 84864592682 scopus 로고    scopus 로고
    • Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma
    • Sun J, Gong X, Purow B, Zhao Z (2012) Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput Biol 8: e1002488.
    • (2012) PLoS Comput Biol , vol.8
    • Sun, J.1    Gong, X.2    Purow, B.3    Zhao, Z.4
  • 10
    • 79959268547 scopus 로고    scopus 로고
    • The implications of relationships between human diseases and metabolic subpathways
    • Li X, Li C, Shang D, Li J, Han J, et al. (2011) The implications of relationships between human diseases and metabolic subpathways. PLoS One 6: e21131.
    • (2011) PLoS One , vol.6
    • Li, X.1    Li, C.2    Shang, D.3    Li, J.4    Han, J.5
  • 11
    • 84868104222 scopus 로고    scopus 로고
    • Characterizing the network of drugs and their affected metabolic subpathways
    • Li C, Shang D, Wang Y, Li J, Han J, et al. (2012) Characterizing the network of drugs and their affected metabolic subpathways. PLoS One 7: e47326.
    • (2012) PLoS One , vol.7
    • Li, C.1    Shang, D.2    Wang, Y.3    Li, J.4    Han, J.5
  • 12
    • 84863265710 scopus 로고    scopus 로고
    • Dissection of human MiRNA regulatory influence to subpathway
    • Li X, Jiang W, Li W, Lian B, Wang S, et al. (2012) Dissection of human MiRNA regulatory influence to subpathway. Brief Bioinform 13: 175-186.
    • (2012) Brief Bioinform , vol.13 , pp. 175-186
    • Li, X.1    Jiang, W.2    Li, W.3    Lian, B.4    Wang, S.5
  • 13
    • 72849108572 scopus 로고    scopus 로고
    • The neuronal microRNA miR-326 acts in a feedback loop with notch and has therapeutic potential against brain tumors
    • Kefas B, Comeau L, Floyd DH, Seleverstov O, Godlewski J, et al. (2009) The neuronal microRNA miR-326 acts in a feedback loop with notch and has therapeutic potential against brain tumors. J Neurosci 29: 15161-15168.
    • (2009) J Neurosci , vol.29 , pp. 15161-15168
    • Kefas, B.1    Comeau, L.2    Floyd, D.H.3    Seleverstov, O.4    Godlewski, J.5
  • 14
    • 78650126775 scopus 로고    scopus 로고
    • Pyruvate kinase M2 is a target of the tumor-suppressive microRNA-326 and regulates the survival of glioma cells
    • Kefas B, Comeau L, Erdle N, Montgomery E, Amos S, et al. (2010) Pyruvate kinase M2 is a target of the tumor-suppressive microRNA-326 and regulates the survival of glioma cells. Neuro Oncol 12: 1102-1112.
    • (2010) Neuro Oncol , vol.12 , pp. 1102-1112
    • Kefas, B.1    Comeau, L.2    Erdle, N.3    Montgomery, E.4    Amos, S.5
  • 15
    • 77956464355 scopus 로고    scopus 로고
    • MiR-221 and miR-222 target PUMA to induce cell survival in glioblastoma
    • Zhang CZ, Zhang JX, Zhang AL, Shi ZD, Han L, et al. (2010) MiR-221 and miR-222 target PUMA to induce cell survival in glioblastoma. Mol Cancer 9: 229.
    • (2010) Mol Cancer , vol.9 , pp. 229
    • Zhang, C.Z.1    Zhang, J.X.2    Zhang, A.L.3    Shi, Z.D.4    Han, L.5
  • 17
    • 79953309923 scopus 로고    scopus 로고
    • A ten-microRNA expression signature predicts survival in glioblastoma
    • Srinivasan S, Patric IR, Somasundaram K (2011) A ten-microRNA expression signature predicts survival in glioblastoma. PLoS One 6: e17438.
    • (2011) PLoS One , vol.6
    • Srinivasan, S.1    Patric, I.R.2    Somasundaram, K.3
  • 18
    • 84891725768 scopus 로고    scopus 로고
    • Whole-genome microRNA expression profiling identifies a 5-microRNA signature as a prognostic biomarker in Chinese patients with primary glioblastoma multiforme
    • Zhang W, Zhang J, Yan W, You G, Bao Z, et al. (2012) Whole-genome microRNA expression profiling identifies a 5-microRNA signature as a prognostic biomarker in Chinese patients with primary glioblastoma multiforme. Cancer.
    • (2012) Cancer
    • Zhang, W.1    Zhang, J.2    Yan, W.3    You, G.4    Bao, Z.5
  • 19
    • 84874512532 scopus 로고    scopus 로고
    • Unique genome-wide map of TCF4 and STAT3 targets using ChIP-seq reveals their association with new molecular subtypes of glioblastoma
    • Zhang JX, Zhang J, Yan W, Wang YY, Han L, et al. (2013) Unique genome-wide map of TCF4 and STAT3 targets using ChIP-seq reveals their association with new molecular subtypes of glioblastoma. Neuro Oncol 15: 279-289.
    • (2013) Neuro Oncol , vol.15 , pp. 279-289
    • Zhang, J.X.1    Zhang, J.2    Yan, W.3    Wang, Y.Y.4    Han, L.5
  • 21
    • 46449115281 scopus 로고    scopus 로고
    • Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma
    • Murat A, Migliavacca E, Gorlia T, Lambiv WL, Shay T, et al. (2008) Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J Clin Oncol 26: 3015-3024.
    • (2008) J Clin Oncol , vol.26 , pp. 3015-3024
    • Murat, A.1    Migliavacca, E.2    Gorlia, T.3    Lambiv, W.L.4    Shay, T.5
  • 22
    • 67650436675 scopus 로고    scopus 로고
    • Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age
    • Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, et al. (2008) Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics 1: 52.
    • (2008) BMC Med Genomics , vol.1 , pp. 52
    • Lee, Y.1    Scheck, A.C.2    Cloughesy, T.F.3    Lai, A.4    Dong, J.5
  • 23
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210. (Pubitemid 34679544)
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 25
    • 77955963884 scopus 로고    scopus 로고
    • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    • Betel D, Koppal A, Agius P, Sander C, Leslie C (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11: R90.
    • (2010) Genome Biol , vol.11
    • Betel, D.1    Koppal, A.2    Agius, P.3    Sander, C.4    Leslie, C.5
  • 27
    • 33748587841 scopus 로고    scopus 로고
    • A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
    • DOI 10.1016/j.cell.2006.07.031, PII S0092867406010993
    • Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, et al. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217. (Pubitemid 44380294)
    • (2006) Cell , vol.126 , Issue.6 , 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
  • 28
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • DOI 10.1261/rna.5248604
    • Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517. (Pubitemid 39288185)
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 29
    • 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 BP, Burge CB, Bartel DP (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
  • 30
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • DOI 10.1038/ng2135, PII NG2135
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284. (Pubitemid 47482690)
    • (2007) Nature Genetics , vol.39 , Issue.10 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 31
    • 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
  • 32
    • 70350000602 scopus 로고    scopus 로고
    • TargetMiner: MicroRNA target prediction with systematic identification of tissue-specific negative examples
    • Bandyopadhyay S, Mitra R (2009) TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 25: 2625-2631.
    • (2009) Bioinformatics , vol.25 , pp. 2625-2631
    • Bandyopadhyay, S.1    Mitra, R.2
  • 35
    • 58149186499 scopus 로고    scopus 로고
    • miRecords: An integrated resource for microRNA-target interactions
    • Xiao F, Zuo Z, Cai G, Kang S, Gao X, et al. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37: D105-110.
    • (2009) Nucleic Acids Res , vol.37
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5
  • 36
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30. (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 37
    • 71049148804 scopus 로고    scopus 로고
    • SubpathwayMiner: A software package for flexible identification of pathways
    • Li C, Li X, Miao Y, Wang Q, Jiang W, et al. (2009) SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res 37: e131.
    • (2009) Nucleic Acids Res , vol.37
    • Li, C.1    Li, X.2    Miao, Y.3    Wang, Q.4    Jiang, W.5
  • 38
    • 84877251556 scopus 로고    scopus 로고
    • Subpathway-GM: Identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways
    • Li C, Han J, Yao Q, Zou C, Xu Y, et al. (2013) Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways. Nucleic Acids Res 41: e101.
    • (2013) Nucleic Acids Res , vol.41
    • Li, C.1    Han, J.2    Yao, Q.3    Zou, C.4    Xu, Y.5
  • 41
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Kohler S, Bauer S, Horn D, Robinson PN (2008) Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82: 949-958.
    • (2008) Am J Hum Genet , vol.82 , pp. 949-958
    • Kohler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 42
    • 77950824571 scopus 로고    scopus 로고
    • Identification and functional characterization of microRNAs involved in the malignant progression of gliomas
    • Malzkorn B, Wolter M, Liesenberg F, Grzendowski M, Stuhler K, et al. (2010) Identification and functional characterization of microRNAs involved in the malignant progression of gliomas. Brain Pathol 20: 539-550.
    • (2010) Brain Pathol , vol.20 , pp. 539-550
    • Malzkorn, B.1    Wolter, M.2    Liesenberg, F.3    Grzendowski, M.4    Stuhler, K.5
  • 43
    • 55549114664 scopus 로고    scopus 로고
    • The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities
    • Bonci D, Coppola V, Musumeci M, Addario A, Giuffrida R, et al. (2008) The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nat Med 14: 1271-1277.
    • (2008) Nat Med , vol.14 , pp. 1271-1277
    • Bonci, D.1    Coppola, V.2    Musumeci, M.3    Addario, A.4    Giuffrida, R.5
  • 44
    • 71549167606 scopus 로고    scopus 로고
    • MiR-15a and MiR-16 control Bmi-1 expression in ovarian cancer
    • Bhattacharya R, Nicoloso M, Arvizo R, Wang E, Cortez A, et al. (2009) MiR-15a and MiR-16 control Bmi-1 expression in ovarian cancer. Cancer Res 69: 9090-9095.
    • (2009) Cancer Res , vol.69 , pp. 9090-9095
    • Bhattacharya, R.1    Nicoloso, M.2    Arvizo, R.3    Wang, E.4    Cortez, A.5
  • 45
    • 77953577606 scopus 로고    scopus 로고
    • Inhibition of STAT3 and ErbB2 suppresses tumor growth, enhances radiosensitivity, and induces mitochondria-dependent apoptosis in glioma cells
    • Gao L, Li F, Dong B, Zhang J, Rao Y, et al. (2010) Inhibition of STAT3 and ErbB2 suppresses tumor growth, enhances radiosensitivity, and induces mitochondria-dependent apoptosis in glioma cells. Int J Radiat Oncol Biol Phys 77: 1223-1231.
    • (2010) Int J Radiat Oncol Biol Phys , vol.77 , pp. 1223-1231
    • Gao, L.1    Li, F.2    Dong, B.3    Zhang, J.4    Rao, Y.5
  • 46
    • 79954414405 scopus 로고    scopus 로고
    • Pro-apoptotic role of integrin beta3 in glioma cells
    • Kim JH, Zheng LT, Lee WH, Suk K (2011) Pro-apoptotic role of integrin beta3 in glioma cells. J Neurochem 117: 494-503.
    • (2011) J Neurochem , vol.117 , pp. 494-503
    • Kim, J.H.1    Zheng, L.T.2    Lee, W.H.3    Suk, K.4
  • 47
    • 84893018348 scopus 로고    scopus 로고
    • Nicotine enhances proliferation, migration, and radioresistance of human malignant glioma cells through EGFR activation
    • Khalil AA, Jameson MJ, Broaddus WC, Lin PS, Chung TD (2012) Nicotine enhances proliferation, migration, and radioresistance of human malignant glioma cells through EGFR activation. Brain Tumor Pathol.
    • (2012) Brain Tumor Pathol
    • Khalil, A.A.1    Jameson, M.J.2    Broaddus, W.C.3    Lin, P.S.4    Chung, T.D.5
  • 48
    • 84866352829 scopus 로고    scopus 로고
    • MiR-410 regulates MET to influence the proliferation and invasion of glioma
    • Chen L, Zhang J, Feng Y, Li R, Sun X, et al. (2012) MiR-410 regulates MET to influence the proliferation and invasion of glioma. Int J Biochem Cell Biol 44: 1711-1717.
    • (2012) Int J Biochem Cell Biol , vol.44 , pp. 1711-1717
    • Chen, L.1    Zhang, J.2    Feng, Y.3    Li, R.4    Sun, X.5
  • 49
    • 0037509990 scopus 로고    scopus 로고
    • Focal adhesion kinase: The first ten years
    • Parsons JT (2003) Focal adhesion kinase: the first ten years. J Cell Sci 116: 1409-1416.
    • (2003) J Cell Sci , vol.116 , pp. 1409-1416
    • Parsons, J.T.1
  • 50
    • 19544383638 scopus 로고    scopus 로고
    • Sample size determination in microarray experiments for class comparison and prognostic classification
    • DOI 10.1093/biostatistics/kxh015
    • Dobbin K, Simon R (2005) Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics 6: 27-38. (Pubitemid 41240367)
    • (2005) Biostatistics , vol.6 , Issue.1 , pp. 27-38
    • Dobbin, K.1    Simon, R.2
  • 51
    • 48249125791 scopus 로고    scopus 로고
    • Malignant gliomas in adults
    • Wen PY, Kesari S (2008) Malignant gliomas in adults. N Engl J Med 359: 492-507.
    • (2008) N Engl J Med , vol.359 , pp. 492-507
    • Wen, P.Y.1    Kesari, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.