메뉴 건너뛰기




Volumn 5, Issue , 2014, Pages

Bridging topological and functional information in protein interaction networks by short loops profiling

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84923319706     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08540     Document Type: Article
Times cited : (19)

References (60)
  • 1
    • 71349087490 scopus 로고    scopus 로고
    • A unifying view of 21st century systems biology
    • Vidal, M. A unifying view of 21st century systems biology. FEBS Letters 583, 3891-3894 (2009).
    • (2009) FEBS Letters , vol.583 , pp. 3891-3894
    • Vidal, M.1
  • 2
    • 33750726771 scopus 로고    scopus 로고
    • Comparison of protein interaction networks reveals species conservation and divergence
    • Liang, Z., Xu, M., Teng, M. & Niu, L. Comparison of protein interaction networks reveals species conservation and divergence. BMC Bioinformatics 7, 457 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 457
    • Liang, Z.1    Xu, M.2    Teng, M.3    Niu, L.4
  • 3
    • 33846608310 scopus 로고    scopus 로고
    • Transcriptional regulation of protein complexes within and across species
    • Tan, K., Shlomi, T., Feizi, H., Ideker, T. & Sharan, R. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci USA 104, 1283-1288 (2007).
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 1283-1288
    • Tan, K.1    Shlomi, T.2    Feizi, H.3    Ideker, T.4    Sharan, R.5
  • 4
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • Vidal, M., Cusick, M. E. & Barabási, A.-L. Interactome networks and human disease. Cell 144, 986-998 (2011).
    • (2011) Cell , vol.144 , pp. 986-998
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.-L.3
  • 5
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker, T. & Sharan, R. Protein networks in disease. Genome Res 18, 644-652 (2008).
    • (2008) Genome Res , vol.18 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 6
    • 84865733409 scopus 로고    scopus 로고
    • The core diseasome
    • Janjić, V. & Przulj, N. The Core Diseasome. Mol Biosyst 8, 2614-2625 (2012).
    • (2012) Mol Biosyst , vol.8 , pp. 2614-2625
    • Janjić, V.1    Przulj, N.2
  • 7
    • 84878242555 scopus 로고    scopus 로고
    • Structural systems pharmacology: The role of 3D structures in next-generation drug development
    • Duran-Frigola, M., Mosca, R. & Aloy, P. Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development. Chem Biol 20, 674-684 (2013).
    • (2013) Chem Biol , vol.20 , pp. 674-684
    • Duran-Frigola, M.1    Mosca, R.2    Aloy, P.3
  • 8
    • 84880993729 scopus 로고    scopus 로고
    • Drug-target interaction prediction through domain-tuned network-based inference
    • Alaimo, S., Pulvirenti, A., Giugno, R. & Ferro, A. Drug-target interaction prediction through domain-tuned network-based inference. Bioinformatics 29, 2004-2008 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2004-2008
    • Alaimo, S.1    Pulvirenti, A.2    Giugno, R.3    Ferro, A.4
  • 9
    • 84863695210 scopus 로고    scopus 로고
    • Prediction of drug-target interactions and drug repositioning via network-based inference
    • Cheng, F. et al. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS computational biology 8, e1002503 (2012).
    • (2012) PLoS Computational Biology , vol.8 , pp. e1002503
    • Cheng, F.1
  • 10
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: A network-based approach to human disease
    • Barabási, A.-L., Gulbahce, N. & Loscalzo, J. Network medicine: a network-based approach to human disease. Nat Rev Genet 12, 56-68 (2011).
    • (2011) Nat Rev Genet , vol.12 , pp. 56-68
    • Barabási, A.-L.1    Gulbahce, N.2    Loscalzo, J.3
  • 11
    • 77957867921 scopus 로고    scopus 로고
    • Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods
    • Fernandes, L. P., Annibale, A., Kleinjung, J., Coolen, A. C. C. & Fraternali, F. Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. PLoS ONE 5 (2010).
    • (2010) PLoS ONE , vol.5
    • Fernandes, L.P.1    Annibale, A.2    Kleinjung, J.3    Coolen, A.C.C.4    Fraternali, F.5
  • 12
    • 84865677098 scopus 로고    scopus 로고
    • A census of human soluble protein complexes
    • Havugimana, P. C. et al. A census of human soluble protein complexes. Cell 150, 1068-1081 (2012).
    • (2012) Cell , vol.150 , pp. 1068-1081
    • Havugimana, P.C.1
  • 13
    • 77956040602 scopus 로고    scopus 로고
    • High-quality binary interactome mapping
    • Dreze, M. et al. High-quality binary interactome mapping. Meth Enzymol 470, 281-315 (2010).
    • (2010) Meth Enzymol , vol.470 , pp. 281-315
    • Dreze, M.1
  • 14
    • 46349091971 scopus 로고    scopus 로고
    • The social network of a cell: Recent advances in interactome mapping
    • Charbonnier, S., Gallego, O. & Gavin, A.-C. The social network of a cell: recent advances in interactome mapping. Biotechnol Annu Rev 14, 1-28 (2008).
    • (2008) Biotechnol Annu Rev , vol.14 , pp. 1-28
    • Charbonnier, S.1    Gallego, O.2    Gavin, A.-C.3
  • 15
    • 84875700843 scopus 로고    scopus 로고
    • Interlaboratory reproducibility of large-scale human proteincomplex analysis by standardized AP-MS
    • Varjosalo, M. et al. Interlaboratory reproducibility of large-scale human proteincomplex analysis by standardized AP-MS. Nat Meth 10, 307-314 (2013).
    • (2013) Nat Meth , vol.10 , pp. 307-314
    • Varjosalo, M.1
  • 16
    • 38049079362 scopus 로고    scopus 로고
    • Protein-protein interaction networks and biology-what's the connection?
    • Hakes, L., Pinney, J. W., Robertson, D. L. & Lovell, S. C. Protein-protein interaction networks and biology-what's the connection? Nature Biotechnology 26, 69-72 (2008).
    • (2008) Nature Biotechnology , vol.26 , pp. 69-72
    • Hakes, L.1    Pinney, J.W.2    Robertson, D.L.3    Lovell, S.C.4
  • 17
    • 78650130580 scopus 로고    scopus 로고
    • Protein-protein interactions: Interactome under construction
    • Bonetta, L. Protein-protein interactions: Interactome under construction. Nature 468, 851-854 (2010).
    • (2010) Nature , vol.468 , pp. 851-854
    • Bonetta, L.1
  • 18
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: Adding structural details to protein networks
    • Mosca, R., Céol, A. & Aloy, P. Interactome3D: adding structural details to protein networks. Nat Meth 10, 47-53 (2013).
    • (2013) Nat Meth , vol.10 , pp. 47-53
    • Mosca, R.1    Céol, A.2    Aloy, P.3
  • 19
    • 84878858665 scopus 로고    scopus 로고
    • INstruct: A database of high-quality 3D structurally resolved protein interactome networks
    • Meyer, M. J., Das, J., Wang, X. & Yu, H. INstruct: a database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics 29, 1577-1579, doi:10.1093/bioinformatics/btt181 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 1577-1579
    • Meyer, M.J.1    Das, J.2    Wang, X.3    Yu, H.4
  • 20
    • 84887939587 scopus 로고    scopus 로고
    • Protein-protein interaction networks studies and importance of 3D structure knowledge
    • Lu, H.-C., Fornili, A. & Fraternali, F. Protein-protein interaction networks studies and importance of 3D structure knowledge. Expert Rev Proteomics 10, 511-520 (2013).
    • (2013) Expert Rev Proteomics , vol.10 , pp. 511-520
    • Lu, H.-C.1    Fornili, A.2    Fraternali, F.3
  • 22
    • 84888681308 scopus 로고    scopus 로고
    • Random graph models and their application to protein-protein interaction networks
    • (eds Stumpf, M.P.H., Balding, D.J. & Girolami, M.). John Wiley & Sons, Ltd, Chichester, UK
    • Higham, D. J. & Pržulj, N. Random Graph Models and Their Application to Protein-Protein Interaction Networks in Handbook of Statistical Systems Biology (eds Stumpf, M. P. H., Balding, D. J. & Girolami, M.). John Wiley & Sons, Ltd, Chichester, UK, 290-308, doi:10.1002/9781119970606.ch14 (2011).
    • (2011) Handbook of Statistical Systems Biology , pp. 290-308
    • Higham, D.J.1    Pržulj, N.2
  • 24
    • 71849108522 scopus 로고    scopus 로고
    • Community detection algorithms: A comparative analysis
    • Lancichinetti, A. & Fortunato, S. Community detection algorithms: A comparative analysis. Physical Review E 80, 056117 (2009).
    • (2009) Physical Review E , vol.80 , pp. 056117
    • Lancichinetti, A.1    Fortunato, S.2
  • 25
    • 13844314048 scopus 로고    scopus 로고
    • Conserved patterns of protein interaction in multiple species
    • Sharan, R. et al. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 102, 1974-1979 (2005).
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 1974-1979
    • Sharan, R.1
  • 26
    • 33748579201 scopus 로고    scopus 로고
    • Interaction graph mining for protein complexes using local clique merging
    • Li, X.-L., Tan, S.-H., Foo, C.-S. & Ng, S.-K. Interaction graph mining for protein complexes using local clique merging. Genome Inform 16, 260-269 (2005).
    • (2005) Genome Inform , vol.16 , pp. 260-269
    • Li, X.-L.1    Tan, S.-H.2    Foo, C.-S.3    Ng, S.-K.4
  • 27
    • 84921298087 scopus 로고    scopus 로고
    • Computational methods for analyzing and modeling biological networks
    • (eds Lonardi, S. & Chen, J.Y.). Chapman & Hall/CRC Data Mining and Knowledge Discovery Series, Chapman and Hall/CRC, Boca Raton, FL
    • Przulj, N. & Milenkovic, T. Computational Methods for Analyzing and Modeling Biological Networks in Biological Data Mining (eds Lonardi, S. & Chen, J. Y.). Chapman & Hall/CRC Data Mining and Knowledge Discovery Series, Chapman and Hall/CRC, Boca Raton, FL, 397-427, doi:10.1201/9781420086850.ch17 (2009).
    • (2009) Biological Data Mining , pp. 397-427
    • Przulj, N.1    Milenkovic, T.2
  • 29
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • Alon, U. Network motifs: theory and experimental approaches. Nat Rev Genet 8, 450-461 (2007).
    • (2007) Nat Rev Genet , vol.8 , pp. 450-461
    • Alon, U.1
  • 30
    • 1942469444 scopus 로고    scopus 로고
    • Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction
    • Yeger-Lotem, E. et al. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 101, 5934-5939 (2004).
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 5934-5939
    • Yeger-Lotem, E.1
  • 31
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824-827 (2002).
    • (2002) Science , vol.298 , pp. 824-827
    • Milo, R.1
  • 32
    • 82555196507 scopus 로고    scopus 로고
    • A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse
    • ra81
    • Carlin, L. M. et al. A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse. Sci Signal 4, ra81 (2011).
    • (2011) Sci Signal , vol.4
    • Carlin, L.M.1
  • 33
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25-29 (2000).
    • (2000) Nature Genetics , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 35
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1
  • 36
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual, J.-F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178 (2005).
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.-F.1
  • 37
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: A resource for annotating the proteome
    • Stelzl, U. et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968 (2005).
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1
  • 38
    • 33947219266 scopus 로고    scopus 로고
    • Large-scale mapping of human protein-protein interactions by mass spectrometry
    • Ewing, R.M. et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 3, 89 (2007).
    • (2007) Mol Syst Biol , vol.3 , pp. 89
    • Ewing, R.M.1
  • 39
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G. D. & Hogue, C. W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003).
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 40
    • 84860361165 scopus 로고    scopus 로고
    • Detecting overlapping protein complexes in protein-protein interaction networks
    • Nepusz, T., Yu, H. & Paccanaro, A. Detecting overlapping protein complexes in protein-protein interaction networks. Nature methods 9, 471-472 (2012).
    • (2012) Nature Methods , vol.9 , pp. 471-472
    • Nepusz, T.1    Yu, H.2    Paccanaro, A.3
  • 41
    • 33749134437 scopus 로고    scopus 로고
    • DExD/H box RNA helicases: Multifunctional proteins with important roles in transcriptional regulation
    • Fuller-Pace, F. V. DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation. Nucleic Acids Res 34, 4206-4215 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. 4206-4215
    • Fuller-Pace, F.V.1
  • 42
    • 0041735083 scopus 로고    scopus 로고
    • Selective regulation of gene expression by nuclear factor 110, a member of the NF90 family of double-stranded RNA-binding proteins
    • Reichman, T. W. et al. Selective regulation of gene expression by nuclear factor 110, a member of the NF90 family of double-stranded RNA-binding proteins. J Mol Biol 332, 85-98 (2003).
    • (2003) J Mol Biol , vol.332 , pp. 85-98
    • Reichman, T.W.1
  • 43
    • 77956175013 scopus 로고    scopus 로고
    • NFAT, immunity and cancer: A transcription factor comes of age
    • Muller, M. R. & Rao, A. NFAT, immunity and cancer: a transcription factor comes of age. Nat Rev Immunol 10, 645-656 (2010).
    • (2010) Nat Rev Immunol , vol.10 , pp. 645-656
    • Muller, M.R.1    Rao, A.2
  • 44
    • 34249063242 scopus 로고    scopus 로고
    • NF90 regulates inducible IL-2 gene expression in T cells
    • Shi, L., Godfrey, W. R., Lin, J., Zhao, G. & Kao, P. N. NF90 regulates inducible IL-2 gene expression in T cells. J Exp Med 204, 971-977 (2007).
    • (2007) J Exp Med , vol.204 , pp. 971-977
    • Shi, L.1    Godfrey, W.R.2    Lin, J.3    Zhao, G.4    Kao, P.N.5
  • 45
    • 40449120728 scopus 로고    scopus 로고
    • Nuclear export of NF90 to stabilize IL-2 mRNA is mediated by AKTdependent phosphorylation at Ser647 in response to CD28 costimulation
    • Pei, Y. et al. Nuclear export of NF90 to stabilize IL-2 mRNA is mediated by AKTdependent phosphorylation at Ser647 in response to CD28 costimulation. J Immunol 180, 222-229 (2008).
    • (2008) J Immunol , vol.180 , pp. 222-229
    • Pei, Y.1
  • 46
    • 58149092016 scopus 로고    scopus 로고
    • Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic RNPs
    • Weidensdorfer, D. et al. Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic RNPs. RNA 15, 104-115 (2009).
    • (2009) RNA , vol.15 , pp. 104-115
    • Weidensdorfer, D.1
  • 47
    • 33744931657 scopus 로고    scopus 로고
    • RNA helicase A is necessary for translation of selected messenger RNAs
    • Hartman, T. R. et al. RNA helicase A is necessary for translation of selected messenger RNAs. Nat Struct Mol Biol 13, 509-516 (2006).
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 509-516
    • Hartman, T.R.1
  • 48
    • 0037634375 scopus 로고    scopus 로고
    • Identification of both shared and distinct proteins in the major and minor spliceosomes
    • Will, C. L., Schneider, C., Reed, R. & Luhrmann, R. Identification of both shared and distinct proteins in the major and minor spliceosomes. Science 284, 2003-2005 (1999).
    • (1999) Science , vol.284 , pp. 2003-2005
    • Will, C.L.1    Schneider, C.2    Reed, R.3    Luhrmann, R.4
  • 49
    • 79957874673 scopus 로고    scopus 로고
    • Next-generation sequencing to generate interactome datasets
    • Yu, H. et al. Next-generation sequencing to generate interactome datasets. Nature methods 8, 478-480 (2011).
    • (2011) Nature Methods , vol.8 , pp. 478-480
    • Yu, H.1
  • 50
    • 58149193222 scopus 로고    scopus 로고
    • Human protein reference database-2009 update
    • Keshava Prasad, T. S. et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 37, D767-772 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. D767-772
    • Keshava Prasad, T.S.1
  • 51
    • 0037062448 scopus 로고    scopus 로고
    • Community structure in social and biological networks
    • Girvan, M. & Newman, M. E. J. Community structure in social and biological networks. Proc Natl Acad Sci USA 99, 7821-7826 (2002).
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7821-7826
    • Girvan, M.1    Newman, M.E.J.2
  • 52
    • 84939882730 scopus 로고    scopus 로고
    • Network motifs that recur across species, including gene regulatory and protein-protein interaction networks
    • Borotkanics, R. & Lehmann, H. Network motifs that recur across species, including gene regulatory and protein-protein interaction networks. Archives of toxicology, 1-11, doi:10.1007/s00204-014-1274-y (2014).
    • (2014) Archives of Toxicology , pp. 1-11
    • Borotkanics, R.1    Lehmann, H.2
  • 54
    • 80052706388 scopus 로고    scopus 로고
    • Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks
    • Michoel, T., Joshi, A., Nachtergaele, B. & Van de Peer, Y. Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. Mol Biosyst 7, 2769-2778 (2011).
    • (2011) Mol Biosyst , vol.7 , pp. 2769-2778
    • Michoel, T.1    Joshi, A.2    Nachtergaele, B.3    Van De-Peer, Y.4
  • 56
    • 84893842910 scopus 로고    scopus 로고
    • Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering
    • Yang, L. & Tang, X. Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering. The Scientific World Journal 2014, 523634 (2014).
    • (2014) The Scientific World Journal , vol.2014 , pp. 523634
    • Yang, L.1    Tang, X.2
  • 57
    • 65449186979 scopus 로고    scopus 로고
    • Fault tolerance in protein interaction networks: Stable bipartite subgraphs and redundant pathways
    • Brady, A., Maxwell, K., Daniels, N. & Cowen, L. J. Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PLoS One 4, e5364 (2009).
    • (2009) PLoS One , vol.4 , pp. e5364
    • Brady, A.1    Maxwell, K.2    Daniels, N.3    Cowen, L.J.4
  • 58
    • 70049106408 scopus 로고    scopus 로고
    • Geometric de-noising of protein-protein interaction networks
    • Kuchaiev, O., Rasajski, M., Higham, D. J. & Przulj, N. Geometric de-noising of protein-protein interaction networks. PLoS computational biology 5, e1000454, doi:10.1371/journal.pcbi.1000454 (2009).
    • (2009) PLoS Computational Biology , vol.5 , pp. e1000454
    • Kuchaiev, O.1    Rasajski, M.2    Higham, D.J.3    Przulj, N.4
  • 59
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5, R80 (2004).
    • (2004) Genome Biol , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 60
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504 (2003).
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.