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Volumn 10, Issue 1, 2012, Pages

Prediction and characterization of protein-protein interaction networks in swine

Author keywords

D MIST; Go annotations; Interolog; M MIST topological properties; Pfam domain annotations; Protein protein interaction network

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; PREDICTIVE VALUE; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; SWINE;

EID: 84862820511     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-10-2     Document Type: Article
Times cited : (19)

References (49)
  • 1
    • 0035369531 scopus 로고    scopus 로고
    • Protein-protein interaction maps: a lead towards cellular functions
    • 10.1016/S0168-9525(01)02323-X, 11377797
    • Legrain P, Wojcik J, Gauthier JM. Protein-protein interaction maps: a lead towards cellular functions. Trends in Genetics 2001, 17(6):346-352. 10.1016/S0168-9525(01)02323-X, 11377797.
    • (2001) Trends in Genetics , vol.17 , Issue.6 , pp. 346-352
    • Legrain, P.1    Wojcik, J.2    Gauthier, J.M.3
  • 3
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • 10.1126/science.285.5428.751, 10427000
    • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285(5428):751-753. 10.1126/science.285.5428.751, 10427000.
    • (1999) Science , vol.285 , Issue.5428 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 7
    • 48249113784 scopus 로고    scopus 로고
    • Predicting and Validating Protein Interactions Using Network Structure
    • Chen PY, Deane CM, Reinert G. Predicting and Validating Protein Interactions Using Network Structure. Plos Computational Biology 2008, 4(7):1-11.
    • (2008) Plos Computational Biology , vol.4 , Issue.7 , pp. 1-11
    • Chen, P.Y.1    Deane, C.M.2    Reinert, G.3
  • 8
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart GT, Ramani AK, Marcotte EM. How complete are current yeast and human protein-interaction networks?. Genome Biology 2006, 7.
    • (2006) Genome Biology , pp. 7
    • Hart, G.T.1    Ramani, A.K.2    Marcotte, E.M.3
  • 10
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions - Two methods for assessment of the reliability of high throughput observations
    • 10.1074/mcp.M100037-MCP200, 22238803
    • Deane CM, Salwinski L, Xenarios I, Eisenberg D. Protein interactions - Two methods for assessment of the reliability of high throughput observations. Molecular & Cellular Proteomics 2002, 1:349-356. 10.1074/mcp.M100037-MCP200, 22238803.
    • (2002) Molecular & Cellular Proteomics , vol.1 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 11
    • 0035211290 scopus 로고    scopus 로고
    • Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs"
    • 10.1101/gr.205301, 311221, 11731503
    • Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Research 2001, 11:2120-2126. 10.1101/gr.205301, 311221, 11731503.
    • (2001) Genome Research , vol.11 , pp. 2120-2126
    • Matthews, L.R.1    Vaglio, P.2    Reboul, J.3    Ge, H.4    Davis, B.P.5    Garrels, J.6    Vincent, S.7    Vidal, M.8
  • 13
    • 38949138554 scopus 로고    scopus 로고
    • Computational prediction of protein-protein interactions
    • 10.1007/s12033-007-0069-2, 18095187
    • Skrabanek L, Saini HK, Bader GD, Enright AJ. Computational prediction of protein-protein interactions. Molecular Biotechnology 2008, 38:1-17. 10.1007/s12033-007-0069-2, 18095187.
    • (2008) Molecular Biotechnology , vol.38 , pp. 1-17
    • Skrabanek, L.1    Saini, H.K.2    Bader, G.D.3    Enright, A.J.4
  • 14
    • 33846086800 scopus 로고    scopus 로고
    • STRING 7 - recent developments in the integration and prediction of protein interactions
    • 10.1093/nar/gkl825, 1669762, 17098935
    • von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P. STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Research 2007, 35:D358-D362. 10.1093/nar/gkl825, 1669762, 17098935.
    • (2007) Nucleic Acids Research , vol.35
    • von Mering, C.1    Jensen, L.J.2    Kuhn, M.3    Chaffron, S.4    Doerks, T.5    Kruger, B.6    Snel, B.7    Bork, P.8
  • 26
    • 57149118625 scopus 로고    scopus 로고
    • Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
    • Kim WK, Marcotte EM. Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence. Plos Computational Biology 2008, 4(11).
    • (2008) Plos Computational Biology , vol.4 , Issue.11
    • Kim, W.K.1    Marcotte, E.M.2
  • 28
    • 50949100075 scopus 로고    scopus 로고
    • Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example
    • 10.1007/s00726-008-0081-2, 18425405
    • Ren LH, Ding YS, Shen YZ, Zhang XF. Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example. Amino Acids 2008, 35:565-572. 10.1007/s00726-008-0081-2, 18425405.
    • (2008) Amino Acids , vol.35 , pp. 565-572
    • Ren, L.H.1    Ding, Y.S.2    Shen, Y.Z.3    Zhang, X.F.4
  • 29
    • 67349200229 scopus 로고    scopus 로고
    • Interaction networks: From protein functions to drug discovery. A review
    • 10.1016/j.patbio.2008.10.004, 19070972
    • Chautard E, Thierry-Mieg N, Ricard-Blum S. Interaction networks: From protein functions to drug discovery. A review. Pathologie Biologie 2009, 57:324-333. 10.1016/j.patbio.2008.10.004, 19070972.
    • (2009) Pathologie Biologie , vol.57 , pp. 324-333
    • Chautard, E.1    Thierry-Mieg, N.2    Ricard-Blum, S.3
  • 30
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • 10.1038/35075138, 11333967
    • Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 31
    • 33846102063 scopus 로고    scopus 로고
    • Proteomics approaches to the systems biology of cardiovascular diseases
    • Drake TA, Ping PP. Proteomics approaches to the systems biology of cardiovascular diseases. Journal of Lipid Research 2007, 48:1-8.
    • (2007) Journal of Lipid Research , vol.48 , pp. 1-8
    • Drake, T.A.1    Ping, P.P.2
  • 32
    • 57149094027 scopus 로고    scopus 로고
    • Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
    • Hegde SR, Manimaran P, Mande SC. Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data. Plos Computational Biology 2008, 4:11.
    • (2008) Plos Computational Biology , vol.4 , pp. 11
    • Hegde, S.R.1    Manimaran, P.2    Mande, S.C.3
  • 33
    • 0035648637 scopus 로고    scopus 로고
    • A faster algorithm for betweenness centrality
    • Brandes U. A faster algorithm for betweenness centrality. Journal of Mathematical Sociology 2001, 25(2):163-177.
    • (2001) Journal of Mathematical Sociology , vol.25 , Issue.2 , pp. 163-177
    • Brandes, U.1
  • 34
    • 13944252976 scopus 로고    scopus 로고
    • A measure of betweenness centrality based on random walks
    • Newman MEJ. A measure of betweenness centrality based on random walks. Social Networks 2005, 27:39-54.
    • (2005) Social Networks , vol.27 , pp. 39-54
    • Newman, M.E.J.1
  • 35
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • 10.1038/nrg1272, 14735121
    • Barabasi AL, Oltvai ZN. Network biology: Understanding the cell's functional organization. Nature Reviews Genetics 2004, 5:101-113. 10.1038/nrg1272, 14735121.
    • (2004) Nature Reviews Genetics , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 36
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • 10.1038/30918, 9623998
    • Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442. 10.1038/30918, 9623998.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 38
    • 57649199632 scopus 로고    scopus 로고
    • The prediction of protein-protein interaction networks in rice blast fungus
    • 10.1186/1471-2164-9-519, 2601049, 18976500
    • He F, Zhang Y, Chen H, Zhang ZD, Peng YL. The prediction of protein-protein interaction networks in rice blast fungus. Bmc Genomics 2008, 9:519. 10.1186/1471-2164-9-519, 2601049, 18976500.
    • (2008) Bmc Genomics , vol.9 , pp. 519
    • He, F.1    Zhang, Y.2    Chen, H.3    Zhang, Z.D.4    Peng, Y.L.5
  • 39
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • 1847944, 17353930
    • Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Molecular Systems Biology 2007, 3:88. 1847944, 17353930.
    • (2007) Molecular Systems Biology , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 40
    • 84875795505 scopus 로고    scopus 로고
    • Uniprot: the Universal Protein Resource
    • Uniprot: the Universal Protein Resource. , http://www.uniprot.org/uniprot
  • 42
    • 13844264506 scopus 로고    scopus 로고
    • IPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    • 10.1093/bioinformatics/bti011, 15353450
    • Finn RD, Marshall M, Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 2005, 21:410-412. 10.1093/bioinformatics/bti011, 15353450.
    • (2005) Bioinformatics , vol.21 , pp. 410-412
    • Finn, R.D.1    Marshall, M.2    Bateman, A.3
  • 43
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Research , vol.13 , 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
  • 44
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • 10.1038/nbt924, 14704708
    • Bader JS, Chaudhuri A, Rothberg JM, Chant J. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnology 2004, 22:78-85. 10.1038/nbt924, 14704708.
    • (2004) Nature Biotechnology , vol.22 , pp. 78-85
    • Bader, J.S.1    Chaudhuri, A.2    Rothberg, J.M.3    Chant, J.4
  • 45
    • 0036279153 scopus 로고    scopus 로고
    • Protein interaction verification and functional annotation by integrated analysis of genome-scale data
    • 10.1016/S1097-2765(02)00531-2, 12049748
    • Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FCP. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Molecular Cell 2002, 9:1133-1143. 10.1016/S1097-2765(02)00531-2, 12049748.
    • (2002) Molecular Cell , vol.9 , pp. 1133-1143
    • Kemmeren, P.1    van Berkum, N.L.2    Vilo, J.3    Bijma, T.4    Donders, R.5    Brazma, A.6    Holstege, F.C.P.7
  • 46
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • 10.1016/S0022-2836(03)00239-0, 12662919
    • Sprinzak E, Sattath S, Margalit H. How reliable are experimental protein-protein interaction data?. Journal of Molecular Biology 2003, 327:919-923. 10.1016/S0022-2836(03)00239-0, 12662919.
    • (2003) Journal of Molecular Biology , vol.327 , pp. 919-923
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 47
    • 0035212065 scopus 로고    scopus 로고
    • Is there a bias in proteome research?
    • 10.1101/gr.206701, 11731485
    • Mrowka R, Patzak A, Herzel H. Is there a bias in proteome research?. Genome Research 2001, 11:1971-1973. 10.1101/gr.206701, 11731485.
    • (2001) Genome Research , vol.11 , pp. 1971-1973
    • Mrowka, R.1    Patzak, A.2    Herzel, H.3
  • 48
    • 84862830633 scopus 로고    scopus 로고
    • A web-based tool for Gene Ontology searching
    • QuickGO
    • QuickGO a web-based tool for Gene Ontology searching. QuickGO., http://www.ebi.ac.uk/QuickGO/
  • 49
    • 34547763236 scopus 로고    scopus 로고
    • A transversal approach to predict gene product networks from ontology-based similarity
    • 10.1186/1471-2105-8-235, 1940024, 17605807
    • Chabalier J, Mosser J, Burgun A. A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics 2007, 8:235. 10.1186/1471-2105-8-235, 1940024, 17605807.
    • (2007) BMC Bioinformatics , vol.8 , pp. 235
    • Chabalier, J.1    Mosser, J.2    Burgun, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.