메뉴 건너뛰기




Volumn 30, Issue 18, 2014, Pages 2627-2635

Mirsynergy: Detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; TRANSCRIPTOME;

EID: 84907483969     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu373     Document Type: Article
Times cited : (77)

References (33)
  • 1
    • 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
  • 2
    • 0035540988 scopus 로고    scopus 로고
    • Np-hard approximation problems in overlapping clustering
    • Barthelemy, J.P. and Brucker, F. (2001) Np-hard approximation problems in overlapping clustering. J. Classif., 18, 159-183.
    • (2001) J. Classif. , vol.18 , pp. 159-183
    • Barthelemy, J.P.1    Brucker, F.2
  • 3
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 4
    • 64549126450 scopus 로고    scopus 로고
    • Human microRNAs co-silence in well-separated groups and have different predicted essentialities
    • Boross, G. et al. (2009) Human microRNAs co-silence in well-separated groups and have different predicted essentialities. Bioinformatics (Oxford, England), 25, 1063-1069.
    • (2009) Bioinformatics (Oxford, England) , vol.25 , pp. 1063-1069
    • Boross, G.1
  • 5
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 6
    • 84899910676 scopus 로고    scopus 로고
    • Induction of epithelial-mesenchymal transition (EMT) in breast cancer cells is calcium signal dependent
    • Davis, F.M. et al. (2013) Induction of epithelial-mesenchymal transition (EMT) in breast cancer cells is calcium signal dependent. Oncogene, 33, 2307-2316.
    • (2013) Oncogene , vol.33 , pp. 2307-2316
    • Davis, F.M.1
  • 7
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes, S.A. et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res., 39, D945-D950.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D945-D950
    • Forbes, S.A.1
  • 8
    • 77950537175 scopus 로고    scopus 로고
    • Regularization paths for generalized linear models via coordinate descent
    • Friedman, J. et al. (2010) Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw., 33, 1-22.
    • (2010) J. Stat. Softw. , vol.33 , pp. 1-22
    • Friedman, J.1
  • 9
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman, R.C. 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
  • 10
    • 84864043341 scopus 로고    scopus 로고
    • Infinite latent feature models and the Indian buffet process
    • MIT Press, Cambridge, Massachusetts, United States
    • Griffiths, T. and Ghahramani, Z. (2005) Infinite latent feature models and the Indian buffet process. In: Advances in Neural Information Processing Systems (NIPS). MIT Press, Cambridge, Massachusetts, United States, pp. 475-482.
    • (2005) Advances in Neural Information Processing Systems (NIPS) , pp. 475-482
    • Griffiths, T.1    Ghahramani, Z.2
  • 11
    • 84876935138 scopus 로고    scopus 로고
    • Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
    • Helwak, A. et al. (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153, 654-665.
    • (2013) Cell , vol.153 , pp. 654-665
    • Helwak, A.1
  • 12
    • 78651266827 scopus 로고    scopus 로고
    • MiRTarBase: A database curates experimentally validated microRNA-target interactions
    • Hsu, S.D. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res., 39, D163-D619.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D163-D619
    • Hsu, S.D.1
  • 13
    • 36749005527 scopus 로고    scopus 로고
    • Using expression profiling data to identify human microRNA targets
    • Huang, J.C. et al. (2007) Using expression profiling data to identify human microRNA targets. Nat. Methods, 4, 1045-1049.
    • (2007) Nat. Methods , vol.4 , pp. 1045-1049
    • Huang, J.C.1
  • 14
    • 84901191625 scopus 로고    scopus 로고
    • Repression of micro RNA-768-3p by MEK/ERK signalling contributes to enhanced mRNA translation in human melanoma
    • Jiang, C.C. et al. (2013) Repression of micro RNA-768-3p by MEK/ERK signalling contributes to enhanced mRNA translation in human melanoma. Oncogene, 33, 2577-2588.
    • (2013) Oncogene , vol.33 , pp. 2577-2588
    • Jiang, C.C.1
  • 15
    • 34249849395 scopus 로고    scopus 로고
    • Discovery of microRNA-mRNA modules via population-based probabilistic learning
    • Joung, J.G et al. (2007) Discovery of microRNA-mRNA modules via population-based probabilistic learning. Bioinformatics (Oxford, England), 23, 1141-1147.
    • (2007) Bioinformatics (Oxford, England) , vol.23 , pp. 1141-1147
    • Joung, J.G.1
  • 16
    • 79957773360 scopus 로고    scopus 로고
    • Small molecules with big effects: The role of the microRNAome in cancer and carcinogenesis
    • Koturbash, I. et al. (2011) Small molecules with big effects: the role of the microRNAome in cancer and carcinogenesis. Mutat. Res., 722, 94-105.
    • (2011) Mutat. Res. , vol.722 , pp. 94-105
    • Koturbash, I.1
  • 17
    • 84891818318 scopus 로고    scopus 로고
    • MiRBase: Annotating high confidence microRNAs using deep sequencing data
    • Kozomara, A and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D68-D73
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 18
    • 20944450160 scopus 로고    scopus 로고
    • Combinatorial microRNA target predictions
    • Krek, A. et al. (2005) Combinatorial microRNA target predictions. Nat. Genet., 37, 495-500.
    • (2005) Nat. Genet. , vol.37 , pp. 495-500
    • Krek, A.1
  • 19
    • 85162507177 scopus 로고    scopus 로고
    • Inferring interaction networks using the ibp applied to microrna target prediction
    • to appear
    • Le, H.S. and Bar-Joseph, Z. (2011) Inferring interaction networks using the ibp applied to microrna target prediction. In: Advances in Neural Information Processing Systems, to appear.
    • (2011) Advances in Neural Information Processing Systems
    • Le, H.S.1    Bar-Joseph, Z.2
  • 20
    • 84879893951 scopus 로고    scopus 로고
    • Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation
    • Le, H.S. and Bar-Joseph, Z. (2013) Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinformatics (Oxford, England), 29, i89-i97.
    • (2013) Bioinformatics (Oxford, England) , vol.29 , pp. i89-i97
    • Le, H.S.1    Bar-Joseph, Z.2
  • 21
    • 80051931399 scopus 로고    scopus 로고
    • A Lasso regression model for the construction of microRNA-target regulatory networks
    • Lu, Y. et al. (2011) A Lasso regression model for the construction of microRNA-target regulatory networks. Bioinformatics (Oxford, England), 27, 2406-2413.
    • (2011) Bioinformatics (Oxford, England) , vol.27 , pp. 2406-2413
    • Lu, Y.1
  • 22
    • 84860361165 scopus 로고    scopus 로고
    • Detecting overlapping protein complexes in protein-protein interaction networks
    • Nepusz, T. et al. (2012) Detecting overlapping protein complexes in protein-protein interaction networks. Nat. Methods, 9, 471-472.
    • (2012) Nat. Methods , vol.9 , pp. 471-472
    • Nepusz, T.1
  • 23
    • 67650754354 scopus 로고    scopus 로고
    • DIANA-mirPath: Integrating human and mouse microRNAs in pathways
    • Papadopoulos, GL. et al. (2009) DIANA-mirPath: Integrating human and mouse microRNAs in pathways. Bioinformatics (Oxford, England), 25, 1991-1993.
    • (2009) Bioinformatics (Oxford, England) , vol.25 , pp. 1991-1993
    • Papadopoulos, G.L.1
  • 24
    • 69549124090 scopus 로고    scopus 로고
    • Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers
    • Peng, X. et al. (2009) Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics, 10, 373.
    • (2009) BMC Genomics , vol.10 , pp. 373
    • Peng, X.1
  • 25
    • 34547555796 scopus 로고    scopus 로고
    • Global and local architecture of the mammalian microRNA-transcription factor regulatory network
    • Shalgi, R. 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 , pp. e131
    • Shalgi, R.1
  • 26
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
    • (2003) Genome Res. , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 27
    • 65249180150 scopus 로고    scopus 로고
    • SnapShot: MicroRNAs in cancer
    • Spizzo, R. et al. (2009) SnapShot: MicroRNAs in cancer. Cell, 137, 586-586.e1.
    • (2009) Cell , vol.137 , pp. 586-586e1
    • Spizzo, R.1
  • 28
    • 78651328883 scopus 로고    scopus 로고
    • The BioGRID Interaction Database: 2011 update
    • Stark, C. et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res., 39, D698-D704.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D698-D704
    • Stark, C.1
  • 29
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 30
    • 77950348609 scopus 로고    scopus 로고
    • Genome-wide dissection of MicroRNA functionsand cotar-geting networks using gene set signatures
    • Tsang, J.S. et al. (2010) Genome-wide dissection of MicroRNA functionsand cotar-geting networks using gene set signatures. Mol. Cell, 38, 140-153.
    • (2010) Mol. Cell , vol.38 , pp. 140-153
    • Tsang, J.S.1
  • 31
    • 0033976586 scopus 로고    scopus 로고
    • TRANSFAC: An integrated system for gene expression regulation
    • Wingender, E. et al. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 316-319
    • Wingender, E.1
  • 32
    • 79951570957 scopus 로고    scopus 로고
    • MiRNA-miRNA synergistic network: Construction via co-regulating functional modules and disease miRNA topological features
    • Xu, J. et al. (2011) MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res., 39, 825-836.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 825-836
    • Xu, J.1
  • 33
    • 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. et al. (2011) A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics (Oxford, England), 27, i401-i409.
    • (2011) Bioinformatics (Oxford, England) , vol.27 , pp. i401-i409
    • Zhang, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.