메뉴 건너뛰기




Volumn 10, Issue 2, 2014, Pages

Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration

Author keywords

[No Author keywords available]

Indexed keywords

DATA ACQUISITION; DATA INTEGRATION;

EID: 84895729123     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003385     Document Type: Review
Times cited : (7)

References (64)
  • 1
    • 77952902183 scopus 로고    scopus 로고
    • Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics
    • Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, et al. (2010) Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 141: 884-896.
    • (2010) Cell , vol.141 , pp. 884-896
    • Nakakuki, T.1    Birtwistle, M.R.2    Saeki, Y.3    Yumoto, N.4    Ide, K.5
  • 2
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
    • (2011) Nucleic Acids Res , vol.39
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4    Roth, A.5
  • 6
    • 58149218155 scopus 로고    scopus 로고
    • Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
    • Simonis N, Rual J-F, Carvunis A-R, Tasan M, Lemmens I, et al. (2009) Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods 6: 47-54.
    • (2009) Nat Methods , vol.6 , pp. 47-54
    • Simonis, N.1    Rual, J.-F.2    Carvunis, A.-R.3    Tasan, M.4    Lemmens, I.5
  • 7
    • 54949120007 scopus 로고    scopus 로고
    • DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
    • Yu J, Pacifico S, Liu G, Finley RL, (2008) DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9: 461.
    • (2008) BMC Genomics , vol.9 , pp. 461
    • Yu, J.1    Pacifico, S.2    Liu, G.3    Finley, R.L.4
  • 8
    • 78651272522 scopus 로고    scopus 로고
    • YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
    • Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Lourenco AB, et al. (2011) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res 39: D136-D140.
    • (2011) Nucleic Acids Res , vol.39
    • Abdulrehman, D.1    Monteiro, P.T.2    Teixeira, M.C.3    Mira, N.P.4    Lourenco, A.B.5
  • 10
    • 78651277460 scopus 로고    scopus 로고
    • PHOSIDA 2011: the posttranslational modification database
    • Gnad F, Gunawardena J, Mann M, (2011) PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res 39: D253-260.
    • (2011) Nucleic Acids Res , vol.39
    • Gnad, F.1    Gunawardena, J.2    Mann, M.3
  • 11
    • 84857047339 scopus 로고    scopus 로고
    • PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, et al. (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 40: D261-270.
    • (2012) Nucleic Acids Res , vol.40
    • Hornbeck, P.V.1    Kornhauser, J.M.2    Tkachev, S.3    Zhang, B.4    Skrzypek, E.5
  • 14
    • 44849086809 scopus 로고    scopus 로고
    • Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites
    • Saunders NFW, Brinkworth RI, Huber T, Kemp BE, Kobe B, (2008) Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. BMC Bioinformatics 9: 245.
    • (2008) BMC Bioinformatics , vol.9 , pp. 245
    • Saunders, N.F.W.1    Brinkworth, R.I.2    Huber, T.3    Kemp, B.E.4    Kobe, B.5
  • 15
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer JC, Cantley LC, Yaffe MB, (2003) Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31: 3635-3641.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 16
    • 33846994717 scopus 로고    scopus 로고
    • EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression
    • Barrasa MI, Vaglio P, Cavasino F, Jacotot L, Walhout AJM, (2007) EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics 8: 21.
    • (2007) BMC Genomics , vol.8 , pp. 21
    • Barrasa, M.I.1    Vaglio, P.2    Cavasino, F.3    Jacotot, L.4    Walhout, A.J.M.5
  • 17
    • 78651335916 scopus 로고    scopus 로고
    • REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
    • Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, et al. (2011) REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res 39: D118-123.
    • (2011) Nucleic Acids Res , vol.39
    • Gallo, S.M.1    Gerrard, D.T.2    Miner, D.3    Simich, M.4    Des Soye, B.5
  • 18
    • 75549083247 scopus 로고    scopus 로고
    • JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
    • Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, et al. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38: D105-110.
    • (2010) Nucleic Acids Res , vol.38
    • Portales-Casamar, E.1    Thongjuea, S.2    Kwon, A.T.3    Arenillas, D.4    Zhao, X.5
  • 19
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489: 91-100.
    • (2012) Nature , vol.489 , pp. 91-100
    • Gerstein, M.B.1    Kundaje, A.2    Hariharan, M.3    Landt, S.G.4    Yan, K.-K.5
  • 20
    • 38549169054 scopus 로고    scopus 로고
    • PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
    • Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, et al. (2007) PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol 8: R207.
    • (2007) Genome Biol , vol.8
    • Portales-Casamar, E.1    Kirov, S.2    Lim, J.3    Lithwick, S.4    Swanson, M.I.5
  • 21
    • 33644875742 scopus 로고    scopus 로고
    • ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
    • Blanco E, Farré D, Albà MM, Messeguer X, Guigó R, (2006) ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Res 34: D63-67.
    • (2006) Nucleic Acids Res , vol.34
    • Blanco, E.1    Farré, D.2    Albà, M.M.3    Messeguer, X.4    Guigó, R.5
  • 23
    • 78651293534 scopus 로고    scopus 로고
    • miRBase: integrating microRNA annotation and deep-sequencing data
    • Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 25
    • 77950820292 scopus 로고    scopus 로고
    • PuTmiR: a database for extracting neighboring transcription factors of human microRNAs
    • Bandyopadhyay S, Bhattacharyya M, (2010) PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics 11: 190.
    • (2010) BMC Bioinformatics , vol.11 , pp. 190
    • Bandyopadhyay, S.1    Bhattacharyya, M.2
  • 26
    • 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, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 27
    • 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
  • 28
    • 75549092303 scopus 로고    scopus 로고
    • TransmiR: a transcription factor-microRNA regulation database
    • Wang J, Lu M, Qiu C, Cui Q, (2010) TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res 38: D119-122.
    • (2010) Nucleic Acids Res , vol.38
    • Wang, J.1    Lu, M.2    Qiu, C.3    Cui, Q.4
  • 33
    • 84856340032 scopus 로고    scopus 로고
    • TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
    • Lepoivre C, Bergon A, Lopez F, Perumal NB, Nguyen C, et al. (2012) TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. BMC Bioinformatics 13: 19.
    • (2012) BMC Bioinformatics , vol.13 , pp. 19
    • Lepoivre, C.1    Bergon, A.2    Lopez, F.3    Perumal, N.B.4    Nguyen, C.5
  • 34
    • 58049194189 scopus 로고    scopus 로고
    • TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database
    • Lopez F, Textoris J, Bergon A, Didier G, Remy E, et al. (2008) TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS ONE 3: e4001.
    • (2008) PLoS ONE , vol.3
    • Lopez, F.1    Textoris, J.2    Bergon, A.3    Didier, G.4    Remy, E.5
  • 35
    • 84872321385 scopus 로고    scopus 로고
    • SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks
    • Fazekas D, Koltai M, Türei D, Módos D, Pálfy M, et al. (2013) SignaLink 2- a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol 7: 7.
    • (2013) BMC Syst Biol , vol.7 , pp. 7
    • Fazekas, D.1    Koltai, M.2    Türei, D.3    Módos, D.4    Pálfy, M.5
  • 36
    • 84880383420 scopus 로고    scopus 로고
    • PharmGKB: The Pharmacogenomics Knowledge Base
    • Thorn CF, Klein TE, Altman RB, (2013) PharmGKB: The Pharmacogenomics Knowledge Base. Methods Mol Biol 1015: 311-320.
    • (2013) Methods Mol Biol , vol.1015 , pp. 311-320
    • Thorn, C.F.1    Klein, T.E.2    Altman, R.B.3
  • 37
  • 38
    • 79960254626 scopus 로고    scopus 로고
    • The Therapeutic Target Database: an internet resource for the primary targets of approved, clinical trial and experimental drugs
    • Liu X, Zhu F, Ma X, Tao L, Zhang J, et al. (2011) The Therapeutic Target Database: an internet resource for the primary targets of approved, clinical trial and experimental drugs. Expert Opin Ther Targets 15: 903-912.
    • (2011) Expert Opin Ther Targets , vol.15 , pp. 903-912
    • Liu, X.1    Zhu, F.2    Ma, X.3    Tao, L.4    Zhang, J.5
  • 40
    • 84859267371 scopus 로고    scopus 로고
    • Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery
    • Zhu F, Shi Z, Qin C, Tao L, Liu X, et al. (2012) Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res 40: D1128-1136.
    • (2012) Nucleic Acids Res , vol.40
    • Zhu, F.1    Shi, Z.2    Qin, C.3    Tao, L.4    Liu, X.5
  • 41
    • 78651287426 scopus 로고    scopus 로고
    • DrugBank 3.0: a comprehensive resource for 'omics' research on drugs
    • Knox C, Law V, Jewison T, Liu P, Ly S, et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res 39: D1035-1041.
    • (2011) Nucleic Acids Res , vol.39
    • Knox, C.1    Law, V.2    Jewison, T.3    Liu, P.4    Ly, S.5
  • 42
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • Blom N, Sicheritz-Pontén T, Gupta R, Gammeltoft S, Brunak S, (2004) Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4: 1633-1649.
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Pontén, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 43
    • 77956664073 scopus 로고    scopus 로고
    • The BioPAX community standard for pathway data sharing
    • Demir E, Cary MP, Paley S, Fukuda K, Lemer C, et al. (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28: 935-942.
    • (2010) Nat Biotechnol , vol.28 , pp. 935-942
    • Demir, E.1    Cary, M.P.2    Paley, S.3    Fukuda, K.4    Lemer, C.5
  • 44
    • 0742323374 scopus 로고    scopus 로고
    • The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data
    • Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, et al. (2004) The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat Biotechnol 22: 177-183.
    • (2004) Nat Biotechnol , vol.22 , pp. 177-183
    • Hermjakob, H.1    Montecchi-Palazzi, L.2    Bader, G.3    Wojcik, J.4    Salwinski, L.5
  • 47
    • 71049143874 scopus 로고    scopus 로고
    • Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains
    • Liu W, Li D, Wang J, Xie H, Zhu Y, et al. (2009) Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. Mol Cell Proteomics 8: 2063-2070.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2063-2070
    • Liu, W.1    Li, D.2    Wang, J.3    Xie, H.4    Zhu, Y.5
  • 48
    • 84877268993 scopus 로고    scopus 로고
    • NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2
    • Turei D, Papp D, Fazekas D, Foldvari-Nagy L, Modos D, et al. (2013) NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. Oxid Med Cell Longev 2013: 737591.
    • (2013) Oxid Med Cell Longev , vol.2013 , pp. 737591
    • Turei, D.1    Papp, D.2    Fazekas, D.3    Foldvari-Nagy, L.4    Modos, D.5
  • 49
    • 84867537553 scopus 로고    scopus 로고
    • CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
    • Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, et al. (2012) CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol 6: 133.
    • (2012) BMC Syst Biol , vol.6 , pp. 133
    • Terfve, C.1    Cokelaer, T.2    Henriques, D.3    MacNamara, A.4    Goncalves, E.5
  • 50
    • 46749130932 scopus 로고    scopus 로고
    • PRINCESS, a protein interaction confidence evaluation system with multiple data sources
    • Li D, Liu W, Liu Z, Wang J, Liu Q, et al. (2008) PRINCESS, a protein interaction confidence evaluation system with multiple data sources. Mol Cell Proteomics 7: 1043-1052.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 1043-1052
    • Li, D.1    Liu, W.2    Liu, Z.3    Wang, J.4    Liu, Q.5
  • 52
    • 78650487946 scopus 로고    scopus 로고
    • HER2 phosphorylation is maintained by a PKB negative feedback loop in response to anti-HER2 herceptin in breast cancer
    • Gijsen M, King P, Perera T, Parker PJ, Harris AL, et al. (2010) HER2 phosphorylation is maintained by a PKB negative feedback loop in response to anti-HER2 herceptin in breast cancer. PLoS Biol 8: e1000563.
    • (2010) PLoS Biol , vol.8
    • Gijsen, M.1    King, P.2    Perera, T.3    Parker, P.J.4    Harris, A.L.5
  • 53
    • 34047174559 scopus 로고    scopus 로고
    • A module of negative feedback regulators defines growth factor signaling
    • Amit I, Citri A, Shay T, Lu Y, Katz M, et al. (2007) A module of negative feedback regulators defines growth factor signaling. Nat Genet 39: 503-512.
    • (2007) Nat Genet , vol.39 , pp. 503-512
    • Amit, I.1    Citri, A.2    Shay, T.3    Lu, Y.4    Katz, M.5
  • 54
    • 78650635354 scopus 로고    scopus 로고
    • The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier
    • Sturm OE, Orton R, Grindlay J, Birtwistle M, Vyshemirsky V, et al. (2010) The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Sci Signal 3: ra90.
    • (2010) Sci Signal , vol.3
    • Sturm, O.E.1    Orton, R.2    Grindlay, J.3    Birtwistle, M.4    Vyshemirsky, V.5
  • 55
    • 84877999280 scopus 로고    scopus 로고
    • Molecular genetic testing and the future of clinical genomics
    • Katsanis SH, Katsanis N, (2013) Molecular genetic testing and the future of clinical genomics. Nat Rev Genet 14: 415-426.
    • (2013) Nat Rev Genet , vol.14 , pp. 415-426
    • Katsanis, S.H.1    Katsanis, N.2
  • 57
    • 84869500366 scopus 로고    scopus 로고
    • Semantic Web meets Integrative Biology: a survey
    • Chen H, Yu T, Chen JY, (2013) Semantic Web meets Integrative Biology: a survey. Brief Bioinform 14: 109-125.
    • (2013) Brief Bioinform , vol.14 , pp. 109-125
    • Chen, H.1    Yu, T.2    Chen, J.Y.3
  • 58
    • 23244465153 scopus 로고    scopus 로고
    • Signaling through receptors and scaffolds: Independent interactions reduce combinatorial complexity
    • Borisov NM, Markevich NI, Hoek JB, Kholodenko BN, (2005) Signaling through receptors and scaffolds: Independent interactions reduce combinatorial complexity. Biophys J 89: 951-966.
    • (2005) Biophys J , vol.89 , pp. 951-966
    • Borisov, N.M.1    Markevich, N.I.2    Hoek, J.B.3    Kholodenko, B.N.4
  • 59
    • 32044464102 scopus 로고    scopus 로고
    • Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains
    • Borisov NM, Markevich NI, Hoek JB, Kholodenko BN, (2006) Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains. Biosystems 83: 152-166.
    • (2006) Biosystems , vol.83 , pp. 152-166
    • Borisov, N.M.1    Markevich, N.I.2    Hoek, J.B.3    Kholodenko, B.N.4
  • 60
    • 84865165310 scopus 로고    scopus 로고
    • Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling
    • Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, et al. (2012) Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Syst Biol 6: 107.
    • (2012) BMC Syst Biol , vol.6 , pp. 107
    • Creamer, M.S.1    Stites, E.C.2    Aziz, M.3    Cahill, J.A.4    Tan, C.W.5
  • 63
    • 79551555393 scopus 로고    scopus 로고
    • Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
    • Sneddon MW, Faeder JR, Emonet T, (2011) Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods 8: 177-183.
    • (2011) Nat Methods , vol.8 , pp. 177-183
    • Sneddon, M.W.1    Faeder, J.R.2    Emonet, T.3
  • 64
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39: D945-950.
    • (2011) Nucleic Acids Res , vol.39
    • Forbes, S.A.1    Bindal, N.2    Bamford, S.3    Cole, C.4    Kok, C.Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.