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Volumn 12, Issue 11, 2013, Pages 3379-3387

ProteoMirExpress: Inferring MicroRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 124; MICRORNA 223;

EID: 84887098104     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O112.019851     Document Type: Article
Times cited : (5)

References (59)
  • 1
    • 60149088848 scopus 로고    scopus 로고
    • Origins and mechanisms of miRNAs and siRNAs
    • Carthew, R. W., and Sontheimer, E. J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655.
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 2
    • 33750370444 scopus 로고    scopus 로고
    • MicroRNA signatures in human cancers
    • DOI 10.1038/nrc1997, PII NRC1997
    • Calin, G. A., and Croce, C. M. (2006) MicroRNA signatures in human cancers. Nature Rev. Cancer 6, 857-866. (Pubitemid 44629897)
    • (2006) Nature Reviews Cancer , vol.6 , Issue.11 , pp. 857-866
    • Calin, G.A.1    Croce, C.M.2
  • 3
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • DOI 10.1261/rna.5248604
    • Rehmsmeier, M., Steffen, P., Hochsmann, M., and 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
  • 4
    • 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., and Segal, E. (2007) The role of site accessibility in micro RNA 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
  • 5
    • 38549124383 scopus 로고    scopus 로고
    • The microRNA.Org resource: Targets and expression
    • DOI 10.1093/nar/gkm995
    • Betel, D., Wilson, M., Gabow, A., Marks, D. S., and Sander, C. (2008) The microRNA.org resource: Targets and expression. Nucleic Acids Res. 36, D149-D153. (Pubitemid 351149712)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Betel, D.1    Wilson, M.2    Gabow, A.3    Marks, D.S.4    Sander, C.5
  • 6
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of Mammalian MicroRNA Targets
    • DOI 10.1016/S0092-8674(03)01018-3
    • Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P., and Burge, C. B. (2003) Prediction of mammalian micro RNA targets. Cell 115, 787-798. (Pubitemid 38058492)
    • (2003) Cell , vol.115 , Issue.7 , pp. 787-798
    • Lewis, B.P.1    Shih, I.-H.2    Jones-Rhoades, M.W.3    Bartel, D.P.4    Burge, C.B.5
  • 8
    • 78651307694 scopus 로고    scopus 로고
    • Star base: A database for exploring micro rna-mrna interaction maps from argonaute clip-seq and degradome-seq data
    • Yang, J. H., Li, J. H., Shao, P., Zhou, H., Chen, Y. Q., and Qu, L. H. (2011) star Base: A database for exploring micro RNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res. 39, D202-D209.
    • (2011) Nucleic Acids Res. , vol.39
    • Yang, J.H.1    Li, J.H.2    Shao, P.3    Zhou, H.4    Chen, Y.Q.5    Qu, L.H.6
  • 9
    • 58149186499 scopus 로고    scopus 로고
    • Mi Records: An integrated resource for micro RNA-target interactions
    • Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., and Li, T. (2009) mi Records: An integrated resource for micro RNA-target 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
  • 11
    • 67849101186 scopus 로고    scopus 로고
    • Micro RNA and mRNA integrated analysis (MMIA): A web tool for examining biological functions of micro RNA expression
    • Nam, S., Li, M., Choi, K., Balch, C., Kim, S., and Nephew, K. P. (2009) Micro RNA and mRNA integrated analysis (MMIA): A web tool for examining biological functions of micro RNA expression. Nucleic Acids Res. 37, W356-W362.
    • (2009) Nucleic Acids Res. , vol.37
    • Nam, S.1    Li, M.2    Choi, K.3    Balch, C.4    Kim, S.5    Nephew, K.P.6
  • 16
    • 79960028760 scopus 로고    scopus 로고
    • Mir act: A web tool for evaluating micro RNA activity based on gene expression data
    • Liang, Z., Zhou, H., He, Z., Zheng, H., and Wu, J. (2011) mir Act: A web tool for evaluating micro RNA activity based on gene expression data. Nucleic Acids Res. 39, W139-W144.
    • (2011) Nucleic Acids Res. , vol.39
    • Liang, Z.1    Zhou, H.2    He, Z.3    Zheng, H.4    Wu, J.5
  • 18
    • 44349128983 scopus 로고    scopus 로고
    • Inferring micro RNA activities by combining gene expression with micro RNA target prediction
    • Cheng, C., and Li, L. M. (2008) Inferring micro RNA activities by combining gene expression with micro RNA target prediction. PloS One 3, e1989.
    • (2008) PloS One , vol.3
    • Cheng, C.1    Li, L.M.2
  • 19
    • 57049175013 scopus 로고    scopus 로고
    • Detecting micro RNA binding and si RNA off-target effects from expression data
    • van Dongen, S., Abreu-Goodger, C., and Enright, A. J. (2008) Detecting micro RNA binding and si RNA off-target effects from expression data. Nat. Methods 5, 1023-1025.
    • (2008) Nat. Methods , vol.5 , pp. 1023-1025
    • Van Dongen, S.1    Abreu-Goodger, C.2    Enright, A.J.3
  • 21
    • 79959997653 scopus 로고    scopus 로고
    • Mir connx: Condition- specific mRNA-micro RNA network integrator
    • Huang, G. T., Athanassiou, C., and Benos, P. V. (2011) mir ConnX: condition- specific mRNA-micro RNA network integrator. Nucleic Acids Res. 39, W416-W423.
    • (2011) Nucleic Acids Res. , vol.39
    • Huang, G.T.1    Athanassiou, C.2    Benos, P.V.3
  • 25
    • 0027730383 scopus 로고
    • Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. Elegans
    • DOI 10.1016/0092-8674(93)90530-4
    • Wightman, B., Ha, I., and Ruvkun, G. (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855-862. (Pubitemid 24014543)
    • (1993) Cell , vol.75 , Issue.5 , pp. 855-862
    • Wightman, B.1    Ha, I.2    Ruvkun, G.3
  • 26
    • 1642366133 scopus 로고    scopus 로고
    • A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development
    • DOI 10.1126/science.1088060
    • Chen, X. (2004) A micro RNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022-2025. (Pubitemid 38393278)
    • (2004) Science , vol.303 , Issue.5666 , pp. 2022-2025
    • Chen, X.1
  • 27
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • DOI 10.1101/gad.1184404
    • Doench, J. G., and Sharp, P. A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511. (Pubitemid 38372808)
    • (2004) Genes and Development , vol.18 , Issue.5 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 28
    • 50849117820 scopus 로고    scopus 로고
    • Importance of translation and nonnucleolytic ago proteins for on-target RNA interference
    • Wu, L., Fan, J., and Belasco, J. G. (2008) Importance of translation and nonnucleolytic ago proteins for on-target RNA interference. Curr. Biol. 18, 1327-1332.
    • (2008) Curr. Biol. , vol.18 , pp. 1327-1332
    • Wu, L.1    Fan, J.2    Belasco, J.G.3
  • 30
    • 84862778053 scopus 로고    scopus 로고
    • Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
    • Bazzini, A. A., Lee, M. T., and Giraldez, A. J. (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233-237.
    • (2012) Science , vol.336 , pp. 233-237
    • Bazzini, A.A.1    Lee, M.T.2    Giraldez, A.J.3
  • 31
    • 84859632747 scopus 로고    scopus 로고
    • MiRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay
    • Djuranovic, S., Nahvi, A., and Green, R. (2012) miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237-240.
    • (2012) Science , vol.336 , pp. 237-240
    • Djuranovic, S.1    Nahvi, A.2    Green, R.3
  • 34
  • 36
    • 78149251209 scopus 로고    scopus 로고
    • Fast Pval: A fast and memory efficient program to calculate very low P-values from empirical distribution
    • Li, M. J., Sham, P. C., and Wang, J. (2010) Fast Pval: A fast and memory efficient program to calculate very low P-values from empirical distribution. Bioinformatics 26, 2897-2899.
    • (2010) Bioinformatics , vol.26 , pp. 2897-2899
    • Li, M.J.1    Sham, P.C.2    Wang, J.3
  • 38
    • 79959930131 scopus 로고    scopus 로고
    • ChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
    • Qin, J., Li, M. J., Wang, P., Zhang, M. Q., and Wang, J. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res. 39, W430-W436.
    • (2011) Nucleic Acids Res. , vol.39
    • Qin, J.1    Li, M.J.2    Wang, P.3    Zhang, M.Q.4    Wang, J.5
  • 39
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software Environment for integrated models of biomolecular interaction networks
    • DOI 10.1101/gr.1239303
    • Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504. (Pubitemid 37428274)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 40
    • 79960917461 scopus 로고    scopus 로고
    • The role of miR-506 in transformed 16HBE cells induced by anti-benzo[a]pyrene-trans-7, 8-dihydrodiol-9, 10-epoxide
    • Zhao, Y., Liu, H., Li, Y., Wu, J., Greenlee, A. R., Yang, C., and Jiang, Y. (2011) The role of miR-506 in transformed 16HBE cells induced by anti-benzo[a]pyrene-trans-7, 8-dihydrodiol-9, 10-epoxide. Toxicol. Lett. 205, 320-326.
    • (2011) Toxicol. Lett. , vol.205 , pp. 320-326
    • Zhao, Y.1    Liu, H.2    Li, Y.3    Wu, J.4    Greenlee, A.R.5    Yang, C.6    Jiang, Y.7
  • 41
    • 70349315533 scopus 로고    scopus 로고
    • Relationships of micro RNA expression in mouse lung with age and exposure to cigarette smoke and light
    • Izzotti, A., Calin, G. A., Steele, V. E., Croce, C. M., and De Flora, S. (2009) Relationships of micro RNA expression in mouse lung with age and exposure to cigarette smoke and light. FASEB J. 23, 3243-3250.
    • (2009) FASEB J. , vol.23 , pp. 3243-3250
    • Izzotti, A.1    Calin, G.A.2    Steele, V.E.3    Croce, C.M.4    De Flora, S.5
  • 45
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 46
    • 44049098715 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture (SILAC)
    • Gruhler, S., and Kratchmarova, I. (2008) Stable isotope labeling by amino acids in cell culture (SILAC). Methods Mol. Biol. 424, 101-111.
    • (2008) Methods Mol. Biol. , vol.424 , pp. 101-111
    • Gruhler, S.1    Kratchmarova, I.2
  • 48
    • 74049115774 scopus 로고    scopus 로고
    • Mass spectrometry-based label-free quantitative proteomics
    • Zhu, W., Smith, J. W., and Huang, C. M. (2010) Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Bio technol. 2010, 840518.
    • (2010) J. Biomed. Bio Technol. 2010 , pp. 840518
    • Zhu, W.1    Smith, J.W.2    Huang, C.M.3
  • 49
    • 4043141477 scopus 로고    scopus 로고
    • Quantitative cancer proteomics: Stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research
    • DOI 10.1074/mcp.M400021-MCP200
    • Everley, P. A., Krijgsveld, J., Zetter, B. R., and Gygi, S. P. (2004) Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell. Proteomics 3, 729-735. (Pubitemid 39077003)
    • (2004) Molecular and Cellular Proteomics , vol.3 , Issue.7 , pp. 729-735
    • Everley, P.A.1    Krijgsveld, J.2    Zetter, B.R.3    Gygi, S.P.4
  • 50
    • 42649132889 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins
    • DOI 10.1074/mcp.M700460-MCP200
    • Graumann, J., Hubner, N. C., Kim, J. B., Ko, K., Moser, M., Kumar, C., Cox, J., Scholer, H., and Mann, M. (2008) Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5, 111 proteins. Mol. Cell. Proteomics 7, 672-683. (Pubitemid 351597479)
    • (2008) Molecular and Cellular Proteomics , vol.7 , Issue.4 , pp. 672-683
    • Graumann, J.1    Hubner, N.C.2    Kim, J.B.3    Ko, K.4    Moser, M.5    Kumar, C.6    Cox, J.7    Scholer, H.8    Mann, M.9
  • 52
    • 26844511378 scopus 로고    scopus 로고
    • Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: A proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acids in cell culture (SILAC)
    • DOI 10.1074/mcp.M500123-MCP200
    • Romijn, E. P., Christis, C., Wieffer, M., Gouw, J. W., Fullaondo, A., van der Sluijs, P., Braakman, I., and Heck, A. J. (2005) Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: A proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acids in cell culture (SILAC). Mol. Cell. Proteomics 4, 1297-1310. (Pubitemid 41448717)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.9 , pp. 1297-1310
    • Romijn, E.P.1    Christis, C.2    Wieffer, M.3    Gouw, J.W.4    Fullaondo, A.5    Van Der Sluijs, P.6    Braakman, I.7    Heck, A.J.R.8
  • 53
    • 79953230529 scopus 로고    scopus 로고
    • Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation
    • M110.000679
    • Tian, R., Wang, S., Elisma, F., Li, L., Zhou, H., Wang, L., and Figeys, D. (2011) Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation. Mol. Cell. Proteomics 10, M110.000679.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Tian, R.1    Wang, S.2    Elisma, F.3    Li, L.4    Zhou, H.5    Wang, L.6    Figeys, D.7
  • 55
    • 63049089189 scopus 로고    scopus 로고
    • Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture
    • Cui, Z., Chen, X., Lu, B., Park, S. K., Xu, T., Xie, Z., Xue, P., Hou, J., Hang, H., Yates, J. R. 3rd, and Yang, F. (2009) Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture. Proteomics 9, 1274-1292.
    • (2009) Proteomics , vol.9 , pp. 1274-1292
    • Cui, Z.1    Chen, X.2    Lu, B.3    Park, S.K.4    Xu, T.5    Xie, Z.6    Xue, P.7    Hou, J.8    Hang, H.9    Yates III, J.R.10    Yang, F.11
  • 57
    • 34249282243 scopus 로고    scopus 로고
    • Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation
    • DOI 10.1038/nature05878, PII NATURE05878
    • Thermann, R., and Hentze, M. W. (2007) Drosophila miR2 induces pseudopolysomes and inhibits translation initiation. Nature 447, 875-878. (Pubitemid 46920140)
    • (2007) Nature , vol.447 , Issue.7146 , pp. 875-878
    • Thermann, R.1    Hentze, M.W.2
  • 58
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian micro RNAs predominantly act to decrease target mRNA levels
    • Guo, H., Ingolia, N. T., Weissman, J. S., and Bartel, D. P. (2010) Mammalian micro RNAs predominantly act to decrease target mRNA levels. Nature 466, 835-840.
    • (2010) Nature , vol.466 , pp. 835-840
    • Guo, H.1    Ingolia, N.T.2    Weissman, J.S.3    Bartel, D.P.4


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