메뉴 건너뛰기




Volumn 12, Issue 10, 2012, Pages 1663-1668

Computational detection of protein complexes in AP-MS experiments

Author keywords

Bioinformatics; Interaction profiling; Protein protein complexes; Systems biology

Indexed keywords

PROTEIN;

EID: 84862705739     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100508     Document Type: Review
Times cited : (9)

References (37)
  • 1
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415, 180-183.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4
  • 2
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin, A. C., Bosche, M., Krause, R., Grandi, P., et al., Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415, 141-147.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4
  • 3
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin, A. C., Aloy, P., Grandi, P., Krause, R., et al., Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440, 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4
  • 4
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan, N. J., Cagney, G., Yu, H., Zhong, G., et al., Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440, 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4
  • 5
    • 79952052352 scopus 로고    scopus 로고
    • iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
    • doi: 10.1093/database/baq023.
    • Turner, B., Razick, S., Turinsky, A. L., Vlasblom, J., et al., iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) 2010, 2010, baq023. doi: 10.1093/database/baq023.
    • (2010) Database (Oxford) , vol.2010
    • Turner, B.1    Razick, S.2    Turinsky, A.L.3    Vlasblom, J.4
  • 7
    • 78650861777 scopus 로고    scopus 로고
    • SAINT: probabilistic scoring of affinity purification-mass spectrometry data
    • Choi, H., Larsen, B., Lin, Z. Y., Breitkreutz, A., et al., SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat. Methods 2011, 8, 70-73.
    • (2011) Nat. Methods , vol.8 , pp. 70-73
    • Choi, H.1    Larsen, B.2    Lin, Z.Y.3    Breitkreutz, A.4
  • 8
    • 67649634849 scopus 로고    scopus 로고
    • Defining the human deubiquitinating enzyme interaction landscape
    • Sowa, M. E., Bennett, E. J., Gygi, S. P., Harper, J. W., Defining the human deubiquitinating enzyme interaction landscape. Cell 2009, 138, 389-403.
    • (2009) Cell , vol.138 , pp. 389-403
    • Sowa, M.E.1    Bennett, E.J.2    Gygi, S.P.3    Harper, J.W.4
  • 10
    • 40349092949 scopus 로고    scopus 로고
    • Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
    • Sardiu, M. E., Cai, Y., Jin, J., Swanson, S. K., et al., Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc. Natl. Acad. Sci. USA 2008, 105, 1454-1459.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 1454-1459
    • Sardiu, M.E.1    Cai, Y.2    Jin, J.3    Swanson, S.K.4
  • 11
    • 34147121646 scopus 로고    scopus 로고
    • Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
    • Collins, S. R., Kemmeren, P., Zhao, X. C., Greenblatt, J. F., et al., Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell Proteomics 2007, 6, 439-450.
    • (2007) Mol. Cell Proteomics , vol.6 , pp. 439-450
    • Collins, S.R.1    Kemmeren, P.2    Zhao, X.C.3    Greenblatt, J.F.4
  • 12
    • 79957575162 scopus 로고    scopus 로고
    • Analysis of the human endogenous coregulator complexome
    • Malovannaya, A., Lanz, R. B., Jung, S. Y., Bulynko, Y., et al., Analysis of the human endogenous coregulator complexome. Cell 2011, 145, 787-799.
    • (2011) Cell , vol.145 , pp. 787-799
    • Malovannaya, A.1    Lanz, R.B.2    Jung, S.Y.3    Bulynko, Y.4
  • 13
    • 41349108025 scopus 로고    scopus 로고
    • From pull-down data to protein interaction networks and complexes with biological relevance
    • Zhang, B., Park, B. H., Karpinets, T., Samatova, N. F., From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 2008, 24, 979-986.
    • (2008) Bioinformatics , vol.24 , pp. 979-986
    • Zhang, B.1    Park, B.H.2    Karpinets, T.3    Samatova, N.F.4
  • 14
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • Albert, R., Scale-free networks in cell biology. J. Cell Sci. 2005, 118, 4947-4957.
    • (2005) J. Cell Sci. , vol.118 , pp. 4947-4957
    • Albert, R.1
  • 16
    • 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 2003, 4, 2.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 17
    • 84862679462 scopus 로고    scopus 로고
    • Graph clustering by flow simulation. PhD Thesis, University of Utrecht, The Netherlands
    • van Dongen, S., Graph clustering by flow simulation. PhD Thesis, University of Utrecht, The Netherlands, 2000.
    • van Dongen, S.1
  • 18
    • 38449114820 scopus 로고    scopus 로고
    • Discovering protein complexes in dense reliable neighborhoods of protein interaction networks
    • Li, X. L., Foo, C. S., Ng, S. K., Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. Comput. Syst. Bioinformatics Conf. 2007, 6, 157-168.
    • (2007) Comput. Syst. Bioinformatics Conf. , vol.6 , pp. 157-168
    • Li, X.L.1    Foo, C.S.2    Ng, S.K.3
  • 19
    • 65849100458 scopus 로고    scopus 로고
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    • Vlasblom, J., Wodak, S. J., Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics 2009, 10, 99.
    • (2009) BMC Bioinformatics , vol.10 , pp. 99
    • Vlasblom, J.1    Wodak, S.J.2
  • 20
    • 20144387067 scopus 로고    scopus 로고
    • The MIPSmammalian protein-protein interaction database
    • Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., et al., The MIPSmammalian protein-protein interaction database. Bioinformatics 2005, 21, 832-834.
    • (2005) Bioinformatics , vol.21 , pp. 832-834
    • Pagel, P.1    Kovac, S.2    Oesterheld, M.3    Brauner, B.4
  • 21
    • 76749150479 scopus 로고    scopus 로고
    • Computational approaches for detecting protein complexes from protein interaction networks: a survey
    • Li, X., Wu, M., Kwoh, C. K., Ng, S. K., Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics 2010, 11(Suppl 1), S3.
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 1
    • Li, X.1    Wu, M.2    Kwoh, C.K.3    Ng, S.K.4
  • 22
    • 67649641077 scopus 로고    scopus 로고
    • A complex-based reconstruction of the Saccharomyces cerevisiae interactome
    • Wang, H., Kakaradov, B., Collins, S. R., Karotki, L., et al., A complex-based reconstruction of the Saccharomyces cerevisiae interactome. Mol. Cell Proteomics 2009, 8, 1361-1381.
    • (2009) Mol. Cell Proteomics , vol.8 , pp. 1361-1381
    • Wang, H.1    Kakaradov, B.2    Collins, S.R.3    Karotki, L.4
  • 23
    • 34547852262 scopus 로고    scopus 로고
    • An ensemble framework for clustering protein-protein interaction networks
    • Asur, S., Ucar, D., Parthasarathy, S., An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 2007, 23, i29-40.
    • (2007) Bioinformatics , vol.23
    • Asur, S.1    Ucar, D.2    Parthasarathy, S.3
  • 24
    • 48249087654 scopus 로고    scopus 로고
    • Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
    • Greene, D., Cagney, G., Krogan, N., Cunningham, P., Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. Bioinformatics 2008, 24, 1722-1728.
    • (2008) Bioinformatics , vol.24 , pp. 1722-1728
    • Greene, D.1    Cagney, G.2    Krogan, N.3    Cunningham, P.4
  • 25
    • 77953077420 scopus 로고    scopus 로고
    • A global protein kinase and phosphatase interaction network in yeast
    • Breitkreutz, A., Choi, H., Sharom, J. R., Boucher, L., et al., A global protein kinase and phosphatase interaction network in yeast. Science 2010, 328, 1043-1046.
    • (2010) Science , vol.328 , pp. 1043-1046
    • Breitkreutz, A.1    Choi, H.2    Sharom, J.R.3    Boucher, L.4
  • 26
    • 33947219266 scopus 로고    scopus 로고
    • Large-scale mapping of human protein-protein interactions by mass spectrometry
    • Ewing, R. M., Chu, P., Elisma, F., Li, H., et al., Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 2007, 3, 89.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 89
    • Ewing, R.M.1    Chu, P.2    Elisma, F.3    Li, H.4
  • 27
    • 80855128256 scopus 로고    scopus 로고
    • Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome
    • Glatter, T., Schittenhelm, R. B., Rinner, O., Roguska, K., et al., Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol. Syst. Biol. 2011, 7, 547.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 547
    • Glatter, T.1    Schittenhelm, R.B.2    Rinner, O.3    Roguska, K.4
  • 28
    • 58549085778 scopus 로고    scopus 로고
    • An integrated workflow for charting the human interaction proteome: insights into the PP2A system
    • Glatter, T., Wepf, A., Aebersold, R., Gstaiger, M., An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol. Syst. Biol. 2009, 5, 237.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 237
    • Glatter, T.1    Wepf, A.2    Aebersold, R.3    Gstaiger, M.4
  • 29
    • 59149096171 scopus 로고    scopus 로고
    • A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein
    • Goudreault, M., D'Ambrosio, L. M., Kean, M. J., Mullin, M. J., et al., A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Mol. Cell Proteomics 2009, 8, 157-171.
    • (2009) Mol. Cell Proteomics , vol.8 , pp. 157-171
    • Goudreault, M.1    D'Ambrosio, L.M.2    Kean, M.J.3    Mullin, M.J.4
  • 30
    • 40349092949 scopus 로고    scopus 로고
    • Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics
    • Sardiu, M. E., Cai, Y., Jin, J., Swanson, S. K., et al., Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc. Natl. Acad. Sci. USA 2008, 105, 1454-1459.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 1454-1459
    • Sardiu, M.E.1    Cai, Y.2    Jin, J.3    Swanson, S.K.4
  • 31
    • 67849097183 scopus 로고    scopus 로고
    • High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNApolymerase II-associated complexes
    • Cloutier, P., Al-Khoury, R., Lavallee-Adam, M., Faubert, D., et al., High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNApolymerase II-associated complexes. Methods 2009, 48, 381-386.
    • (2009) Methods , vol.48 , pp. 381-386
    • Cloutier, P.1    Al-Khoury, R.2    Lavallee-Adam, M.3    Faubert, D.4
  • 32
    • 77952226764 scopus 로고    scopus 로고
    • Super-SILACmix for quantitative proteomics of human tumor tissue
    • Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J. R., et al., Super-SILACmix for quantitative proteomics of human tumor tissue. Nat. Methods 2010, 7, 383-385.
    • (2010) Nat. Methods , vol.7 , pp. 383-385
    • Geiger, T.1    Cox, J.2    Ostasiewicz, P.3    Wisniewski, J.R.4
  • 33
    • 65249180173 scopus 로고    scopus 로고
    • An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency
    • Ho, L., Ronan, J. L., Wu, J., Staahl, B. T., et al., An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc. Natl. Acad. Sci. USA 2009, 106, 5181-5186.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 5181-5186
    • Ho, L.1    Ronan, J.L.2    Wu, J.3    Staahl, B.T.4
  • 34
    • 0034782618 scopus 로고    scopus 로고
    • Model-based clustering and data transformation for gene expression data
    • Yeung, K., Fraley, C., Murua, A., Raftery, A., et al., Model-based clustering and data transformation for gene expression data. Bioinformatics 2001, 17, 977-987.
    • (2001) Bioinformatics , vol.17 , pp. 977-987
    • Yeung, K.1    Fraley, C.2    Murua, A.3    Raftery, A.4
  • 36
    • 67049118963 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein complex and protein interaction network assembly
    • Sardiu, M. E., Florens, L., Washburn, M. P., Evaluation of clustering algorithms for protein complex and protein interaction network assembly. J. Proteome Res. 2009, 8, 2944-2952.
    • (2009) J. Proteome Res. , vol.8 , pp. 2944-2952
    • Sardiu, M.E.1    Florens, L.2    Washburn, M.P.3
  • 37
    • 77953994414 scopus 로고    scopus 로고
    • Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data
    • Choi, H., Kim, S., Gingras, A. C., Nesvizhskii, A. I., Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. Mol. Syst. Biol. 2010, 6, 385.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 385
    • Choi, H.1    Kim, S.2    Gingras, A.C.3    Nesvizhskii, A.I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.