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Volumn 12, Issue 6, 2013, Pages 1689-1700

Proteome-wide prediction of self-interacting proteins based on multiple properties

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; PROTEOME;

EID: 84878730589     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M112.021790     Document Type: Article
Times cited : (32)

References (49)
  • 1
    • 79956188298 scopus 로고    scopus 로고
    • Caught in self-interaction: Evolutionary and functional mechanisms of protein homooligomerization
    • Hashimoto, K., Nishi, H., Bryant, S., and Panchenko, A. R. (2011) Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. Phys. Biol. 8, 035007
    • (2011) Phys. Biol. , vol.8 , pp. 035007
    • Hashimoto, K.1    Nishi, H.2    Bryant, S.3    Panchenko, A.R.4
  • 2
    • 6344260294 scopus 로고    scopus 로고
    • The power of two: Protein dimerization in biology
    • DOI 10.1016/j.tibs.2004.09.006, PII S0968000404002348
    • Marianayagam, N. J., Sunde, M., and Matthews, J. M. (2004) The power of two: protein dimerization in biology. Trends Biochem. Sci. 29, 618-625 (Pubitemid 39389082)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.11 , pp. 618-625
    • Marianayagam, N.J.1    Sunde, M.2    Matthews, J.M.3
  • 3
    • 21244464335 scopus 로고    scopus 로고
    • Binding properties and evolution of homodimers in protein-protein interaction networks
    • DOI 10.1093/nar/gki678
    • Ispolatov, I., Yuryev, A., Mazo, I., and Maslov, S. (2005) Binding properties and evolution of homodimers in protein-protein interaction networks. Nucleic Acids Res. 33, 3629-3635 (Pubitemid 41430585)
    • (2005) Nucleic Acids Research , vol.33 , Issue.11 , pp. 3629-3635
    • Ispolatov, I.1    Yuryev, A.2    Mazo, I.3    Maslov, S.4
  • 5
    • 47649121227 scopus 로고    scopus 로고
    • Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm
    • DOI 10.1093/molbev/msn122
    • Chen, Y., and Dokholyan, N. V. (2008) Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Mol. Biol. Evol. 25, 1530-1533 (Pubitemid 352019857)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.8 , pp. 1530-1533
    • Chen, Y.1    Dokholyan, N.V.2
  • 8
    • 59049100728 scopus 로고    scopus 로고
    • Questioning the ubiquity of neofunctionalization
    • Gibson, T. A., and Goldberg, D. S. (2009) Questioning the ubiquity of neofunctionalization. PLoS Comput. Biol. 5, e1000252
    • (2009) PLoS Comput. Biol. , vol.5
    • Gibson, T.A.1    Goldberg, D.S.2
  • 9
    • 34848913963 scopus 로고    scopus 로고
    • Evolution of protein complexes by duplication of homomeric interactions
    • Pereira-Leal, J. B., Levy, E. D., Kamp, C., and Teichmann, S. A. (2007) Evolution of protein complexes by duplication of homomeric interactions. Genome Biol. 8, R51
    • (2007) Genome Biol , vol.8
    • Pereira-Leal, J.B.1    Levy, E.D.2    Kamp, C.3    Teichmann, S.A.4
  • 16
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the Universal Protein Resource
    • UniProt Consortium
    • UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 9, D214-D219
    • (2011) Nucleic Acids Res. , vol.9
  • 19
    • 44349158988 scopus 로고    scopus 로고
    • How many human genes can be defined as housekeeping with current expression data?
    • Zhu, J., He, F., Song, S., Wang, J., and Yu, J. (2008) How many human genes can be defined as housekeeping with current expression data? BMC Genomics 9, 172
    • (2008) BMC Genomics , vol.9 , pp. 172
    • Zhu, J.1    He, F.2    Song, S.3    Wang, J.4    Yu, J.5
  • 24
    • 79956201211 scopus 로고    scopus 로고
    • Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs
    • Liu, Z., Liu, Q., Sun, H., Hou, L., Guo, H., Zhu, Y., Li, D., and He, F. (2011) Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. BMC Evol. Biol. 11, 133
    • (2011) BMC Evol. Biol. , vol.11 , pp. 133
    • Liu, Z.1    Liu, Q.2    Sun, H.3    Hou, L.4    Guo, H.5    Zhu, Y.6    Li, D.7    He, F.8
  • 25
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • DOI 10.1155/JBB.2005.96
    • Joy, M. P., Brock, A., Ingber, D. E., and Huang, S. (2005) High between ness proteins in the yeast protein interaction network. J. Biomed. Biotechnol. 2005, 96-103 (Pubitemid 41627865)
    • (2005) Journal of Biomedicine and Biotechnology , vol.2005 , Issue.2 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 26
    • 17644384367 scopus 로고    scopus 로고
    • Minimum redundancy feature selection from microarray gene expression data
    • DOI 10.1142/S0219720005001004, PII S0219720005001004
    • Ding, C., and Peng, H. (2005) Minimum redundancy feature selection from microarray gene expression data. J. Bioinform. Comput. Biol. 3, 185-205 (Pubitemid 40561382)
    • (2005) Journal of Bioinformatics and Computational Biology , vol.3 , Issue.2 , pp. 185-205
    • Ding, C.1    Peng, H.2
  • 27
    • 77950448057 scopus 로고    scopus 로고
    • Predicting drug-target interaction networks based on functional groups and biological features
    • He, Z., Zhang, J., Shi, X. H., Hu, L. L., Kong, X., Cai, Y. D., and Chou, K. C. (2010) Predicting drug-target interaction networks based on functional groups and biological features. PLoS One 5, e9603
    • (2010) PLoS One , vol.5
    • He, Z.1    Zhang, J.2    Shi, X.H.3    Hu, L.L.4    Kong, X.5    Cai, Y.D.6    Chou, K.C.7
  • 28
    • 13244267007 scopus 로고    scopus 로고
    • Estimating mutual information using B-spline functions-an improved similarity measure for analysing gene expression data
    • Daub, C. O., Steuer, R., Selbig, J., and Kloska, S. (2004) Estimating mutual information using B-spline functions-an improved similarity measure for analysing gene expression data. BMC Bioinformatics 5, 118
    • (2004) BMC Bioinformatics , vol.5 , pp. 118
    • Daub, C.O.1    Steuer, R.2    Selbig, J.3    Kloska, S.4
  • 29
    • 13244265581 scopus 로고    scopus 로고
    • Information assessment on predicting protein-protein interactions
    • Lin, N., Wu, B., Jansen, R., Gerstein, M., and Zhao, H. (2004) Information assessment on predicting protein-protein interactions. BMC Bioinformatics 5, 154
    • (2004) BMC Bioinformatics , vol.5 , pp. 154
    • Lin, N.1    Wu, B.2    Jansen, R.3    Gerstein, M.4    Zhao, H.5
  • 30
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team. R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
    • (2009) R: A Language and Environment for Statistical Computing
  • 31
    • 46749130932 scopus 로고    scopus 로고
    • PRINCESS, a protein interaction confidence evaluation system with multiple data sources
    • DOI 10.1074/mcp.M700287-MCP200
    • Li, D., Liu, W., Liu, Z., Wang, J., Liu, Q., Zhu, Y., and He, F. (2008) PRINCESS, a protein interaction confidence evaluation system with multiple data sources. Mol. Cell. Proteomics 7, 1043-1052 (Pubitemid 351943952)
    • (2008) Molecular and Cellular Proteomics , vol.7 , Issue.6 , pp. 1043-1052
    • Li, D.1    Liu, W.2    Liu, Z.3    Wang, J.4    Liu, Q.5    Zhu, Y.6    He, F.7
  • 32
    • 0003469193 scopus 로고    scopus 로고
    • SPSS Inc., SPSS, Inc., Chicago
    • SPSS, Inc. (1999) SPSS Base 10.0, User's Guide, pp. 431-434, SPSS, Inc., Chicago
    • (1999) SPSS Base 10.0, User's Guide , pp. 431-434
  • 33
    • 84864661612 scopus 로고    scopus 로고
    • General trends in the utilization of structural factors contributing to biological complexity
    • Yang, D., Zhong, F., Li, D., Liu, Z., Wei, H., Jiang, Y., and He, F. (2012) General trends in the utilization of structural factors contributing to biological complexity. Mol. Biol. Evol. 29, 1957-1968
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1957-1968
    • Yang, D.1    Zhong, F.2    Li, D.3    Liu, Z.4    Wei, H.5    Jiang, Y.6    He, F.7
  • 34
    • 33749337098 scopus 로고    scopus 로고
    • The many faces of protein-protein interactions: A compendium of interface geometry
    • Kim, W. K., Henschel, A., Winter, C., and Schroeder, M. (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput. Biol. 2, e124
    • (2006) PLoS Comput. Biol. , vol.2
    • Kim, W.K.1    Henschel, A.2    Winter, C.3    Schroeder, M.4
  • 35
    • 57149118625 scopus 로고    scopus 로고
    • Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence
    • Kim, W. K., and Marcotte, E. M. (2008) Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PLoS Comput. Biol. 4, e1000232
    • (2008) PLoS Comput. Biol. , vol.4
    • Kim, W.K.1    Marcotte, E.M.2
  • 36
    • 33748304130 scopus 로고    scopus 로고
    • Protein bipartivity and essentiality in the yeast protein-protein interaction network
    • DOI 10.1021/pr060106e
    • Estrada, E. (2006) Protein bipartivity and essentiality in the yeast protein protein interaction network. J. Proteome Res. 5, 2177-2184 (Pubitemid 44330810)
    • (2006) Journal of Proteome Research , vol.5 , Issue.9 , pp. 2177-2184
    • Estrada, E.1
  • 38
    • 1642513708 scopus 로고    scopus 로고
    • Conservation of proteinprotein interactions-lessons from ascomycota
    • Pagel, P., Mewes, H. W., and Frishman, D. (2004) Conservation of proteinprotein interactions-lessons from ascomycota. Trends Genet. 20, 72-76
    • (2004) Trends Genet , vol.20 , pp. 72-76
    • Pagel, P.1    Mewes, H.W.2    Frishman, D.3
  • 40
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: Criteria of Max-Dependency, Max-Relevance, and Min-Redundancy
    • DOI 10.1109/TPAMI.2005.159
    • Peng, H., Long, F., and Ding, C. (2005) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell. 27, 1226-1238 (Pubitemid 41245053)
    • (2005) IEEE Transactions on Pattern Analysis and Machine Intelligence , vol.27 , Issue.8 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 41
    • 33644746460 scopus 로고    scopus 로고
    • Integrated prediction of the helical membrane protein interactome in yeast
    • DOI 10.1016/j.jmb.2005.12.067, PII S0022283605016438
    • Xia, Y., Lu, L. J., and Gerstein, M. (2006) Integrated prediction of the helical membrane protein interactome in yeast. J. Mol. Biol. 357, 339-349 (Pubitemid 43339335)
    • (2006) Journal of Molecular Biology , vol.357 , Issue.1 , pp. 339-349
    • Xia, Y.1    Lu, L.J.2    Gerstein, M.3
  • 42
    • 67650904949 scopus 로고    scopus 로고
    • Integrated assessment of genomic correlates of protein evolutionary rate
    • Xia, Y., Franzosa, E. A., and Gerstein, M. B. (2009) Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Comput. Biol. 5, e1000413
    • (2009) PLoS Comput. Biol. , vol.5
    • Xia, Y.1    Franzosa, E.A.2    Gerstein, M.B.3
  • 43
    • 0030695445 scopus 로고    scopus 로고
    • The maturity-onset diabetes of the young (MODY1) transcription factor HNF4α regulates expression of genes required for glucose transport and metabolism
    • DOI 10.1073/pnas.94.24.13209
    • Stoffel, M., and Duncan, S. A. (1997) The maturity-onset diabetes of the young (MODY1) transcription factor HNF4 regulates expression of genes required for glucose transport and metabolism. Proc. Natl. Acad. Sci. U.S.A. 94, 13209-13214 (Pubitemid 27518501)
    • (1997) Proceedings of the National Academy of Sciences of the United States of America , vol.94 , Issue.24 , pp. 13209-13214
    • Stoffel, M.1    Duncan, S.A.2
  • 44
    • 10344239412 scopus 로고    scopus 로고
    • Netrin-1 and its receptors in tumorigenesis
    • DOI 10.1038/nrc1504
    • Arakawa, H. (2004) Netrin-1 and its receptors in tumorigenesis. Nat. Rev. Cancer 4, 978-987 (Pubitemid 39626221)
    • (2004) Nature Reviews Cancer , vol.4 , Issue.12 , pp. 978-987
    • Arakawa, H.1
  • 45
    • 0037177560 scopus 로고    scopus 로고
    • Evolutionary rate in the protein interaction network
    • DOI 10.1126/science.1068696
    • Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C., and Feldman, M. W. (2002) Evolutionary rate in the protein interaction network. Science 296, 750-752 (Pubitemid 34442006)
    • (2002) Science , vol.296 , Issue.5568 , pp. 750-752
    • Fraser, H.B.1    Hirsh, A.E.2    Steinmetz, L.M.3    Scharfe, C.4    Feldman, M.W.5
  • 46
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • DOI 10.1093/molbev/msi072
    • Hahn, M. W., and Kern, A. D. (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol. 22, 803-806 (Pubitemid 40471393)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.4 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 47
    • 0642285840 scopus 로고    scopus 로고
    • Preferential attachment in the protein network evolution
    • Eisenberg, E., and Levanon, E. Y. (2003) Preferential attachment in the protein network evolution. Phys. Rev. Lett. 91, 138701
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 138701
    • Eisenberg, E.1    Levanon, E.Y.2
  • 48
    • 33644897576 scopus 로고    scopus 로고
    • Further understanding human disease genes by comparing with housekeeping genes and other genes
    • Tu, Z., Wang, L., Xu, M., Zhou, X., Chen, T., and Sun, F. (2006) Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics 7, 31
    • (2006) BMC Genomics , vol.7 , pp. 31
    • Tu, Z.1    Wang, L.2    Xu, M.3    Zhou, X.4    Chen, T.5    Sun, F.6
  • 49
    • 73549090972 scopus 로고    scopus 로고
    • Structure of protein interaction networks and their implications on drug design
    • Hase, T., Tanaka, H., Suzuki, Y., Nakagawa, S., and Kitano, H. (2009) Structure of protein interaction networks and their implications on drug design. PLoS Comput. Biol. 5, e1000550
    • (2009) PLoS Comput. Biol. , vol.5
    • Hase, T.1    Tanaka, H.2    Suzuki, Y.3    Nakagawa, S.4    Kitano, H.5


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