메뉴 건너뛰기




Volumn 7, Issue , 2013, Pages

A novel function prediction approach using protein overlap networks

Author keywords

Composite network; Functional genomics; Protein function prediction; Protein overlap network

Indexed keywords

PROTEIN;

EID: 84880182330     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-61     Document Type: Article
Times cited : (20)

References (45)
  • 1
    • 0034660322 scopus 로고    scopus 로고
    • Protein function in the post-genomic era
    • 10.1038/35015694, 10866208
    • Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature 2000, 405:823-826. 10.1038/35015694, 10866208.
    • (2000) Nature , vol.405 , pp. 823-826
    • Eisenberg, D.1    Marcotte, E.M.2    Xenarios, I.3    Yeates, T.O.4
  • 2
    • 3242773098 scopus 로고    scopus 로고
    • Prediction of protein function in the absence of significant sequence similarity
    • 10.2174/0929867043364702, 15279553
    • Dobson PD, Cai YD, Stapley BJ, Doig AJ. Prediction of protein function in the absence of significant sequence similarity. Curr Med Chem 2004, 11:2135-2142. 10.2174/0929867043364702, 15279553.
    • (2004) Curr Med Chem , vol.11 , pp. 2135-2142
    • Dobson, P.D.1    Cai, Y.D.2    Stapley, B.J.3    Doig, A.J.4
  • 3
    • 77649249353 scopus 로고    scopus 로고
    • Visualization of multiple alignments, phylogenies and gene family evolution
    • 10.1038/nmeth.1434, 20195253
    • Procter JB, Thompson J, Letunic I, Creevey C, Jossinet F, Barton GJ. Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods 2010, 7:S16-S25. 10.1038/nmeth.1434, 20195253.
    • (2010) Nat Methods , vol.7
    • Procter, J.B.1    Thompson, J.2    Letunic, I.3    Creevey, C.4    Jossinet, F.5    Barton, G.J.6
  • 4
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • 10.1016/j.sbi.2005.04.003, 15963890
    • Watson JD, Laskowski RA, Thornton JM. Predicting protein function from sequence and structural data. Curr Opin Struct Biol 2005, 15:275-284. 10.1016/j.sbi.2005.04.003, 15963890.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 275-284
    • Watson, J.D.1    Laskowski, R.A.2    Thornton, J.M.3
  • 5
    • 11844292002 scopus 로고    scopus 로고
    • Inference of protein function from protein structure
    • 10.1016/j.str.2004.10.015, 15642267
    • Pal D, Eisenberg D. Inference of protein function from protein structure. Structure 2005, 13:121-130. 10.1016/j.str.2004.10.015, 15642267.
    • (2005) Structure , vol.13 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 6
    • 13944252921 scopus 로고    scopus 로고
    • Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology
    • 10.1002/prot.20355, 15645518
    • Ponomarenko JV, Bourne PE, Shindyalov IN. Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins 2005, 58:855-865. 10.1002/prot.20355, 15645518.
    • (2005) Proteins , vol.58 , pp. 855-865
    • Ponomarenko, J.V.1    Bourne, P.E.2    Shindyalov, I.N.3
  • 7
    • 84864593192 scopus 로고    scopus 로고
    • Structure- and sequence-based function prediction for non-homologous proteins
    • 10.1007/s10969-012-9126-6, 3375349, 22270458
    • Sael L, Chitale M, Kihara D. Structure- and sequence-based function prediction for non-homologous proteins. J Struct Funct Genomics 2012, 13:111-123. 10.1007/s10969-012-9126-6, 3375349, 22270458.
    • (2012) J Struct Funct Genomics , vol.13 , pp. 111-123
    • Sael, L.1    Chitale, M.2    Kihara, D.3
  • 8
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • 10.1016/j.jmb.2003.08.057, 14568541
    • Tian W, Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J Mol Biol 2003, 333:863-882. 10.1016/j.jmb.2003.08.057, 14568541.
    • (2003) J Mol Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 9
    • 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. Mol Syst Biol 2007, 3:88. 1847944, 17353930.
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 10
    • 78650539578 scopus 로고    scopus 로고
    • Network-based function prediction and interactomics: the case for metabolic enzymes
    • 10.1016/j.ymben.2010.07.001, 20654726
    • Janga SC, Diaz-Mejia JJ, Moreno-Hagelsieb G. Network-based function prediction and interactomics: the case for metabolic enzymes. Metab Eng 2011, 13:1-10. 10.1016/j.ymben.2010.07.001, 20654726.
    • (2011) Metab Eng , vol.13 , pp. 1-10
    • Janga, S.C.1    Diaz-Mejia, J.J.2    Moreno-Hagelsieb, G.3
  • 11
    • 84864579478 scopus 로고    scopus 로고
    • Domain-mediated protein interaction prediction: From genome to network
    • 10.1016/j.febslet.2012.04.027, 22561014
    • Reimand J, Hui S, Jain S, Law B, Bader GD. Domain-mediated protein interaction prediction: From genome to network. FEBS Lett 2012, 586:2751-2763. 10.1016/j.febslet.2012.04.027, 22561014.
    • (2012) FEBS Lett , vol.586 , pp. 2751-2763
    • Reimand, J.1    Hui, S.2    Jain, S.3    Law, B.4    Bader, G.D.5
  • 12
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • 10.1038/82360, 11101803
    • Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18:1257-1261. 10.1038/82360, 11101803.
    • (2000) Nat Biotechnol , vol.18 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 13
    • 0035044077 scopus 로고    scopus 로고
    • Assessment of prediction accuracy of protein function from protein-protein interaction data
    • 10.1002/yea.706, 11284008
    • Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 2001, 18:523-531. 10.1002/yea.706, 11284008.
    • (2001) Yeast , vol.18 , pp. 523-531
    • Hishigaki, H.1    Nakai, K.2    Ono, T.3    Tanigami, A.4    Takagi, T.5
  • 14
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • 10.1093/bioinformatics/btl145, 16632496
    • Chua HN, Sung WK, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22:1623-1630. 10.1093/bioinformatics/btl145, 16632496.
    • (2006) Bioinformatics , vol.22 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.K.2    Wong, L.3
  • 15
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • 10.1073/pnas.2032324100, 218723, 14517352
    • Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003, 100:12123-12128. 10.1073/pnas.2032324100, 218723, 14517352.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 16
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • 10.1073/pnas.0237338100, 298738, 12538875
    • Rives AW, Galitski T. Modular organization of cellular networks. Proc Natl Acad Sci USA 2003, 100:1128-1133. 10.1073/pnas.0237338100, 298738, 12538875.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 17
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinforma 2003, 4:2.
    • (2003) BMC Bioinforma , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 18
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinforma 2006, 7:207.
    • (2006) BMC Bioinforma , vol.7 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 19
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal JB, Enright AJ, Ouzounis CA. Detection of functional modules from protein interaction networks. Proteins 2004, 54:49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3
  • 20
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • 10.1038/340245a0, 2547163
    • Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989, 340:245-246. 10.1038/340245a0, 2547163.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 21
    • 0018790602 scopus 로고
    • Affinity precipitation of enzymes
    • 10.1016/0014-5793(79)80211-2, 217735
    • Larsson PO, Mosbach K. Affinity precipitation of enzymes. FEBS Lett 1979, 98:333-338. 10.1016/0014-5793(79)80211-2, 217735.
    • (1979) FEBS Lett , vol.98 , pp. 333-338
    • Larsson, P.O.1    Mosbach, K.2
  • 22
    • 0024549504 scopus 로고
    • Suppressors of yeast actin mutations
    • 1203651, 2656401
    • Novick P, Osmond BC, Botstein D. Suppressors of yeast actin mutations. Genetics 1989, 121:659-674. 1203651, 2656401.
    • (1989) Genetics , vol.121 , pp. 659-674
    • Novick, P.1    Osmond, B.C.2    Botstein, D.3
  • 23
    • 0025959707 scopus 로고
    • Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae
    • 369400, 1996092
    • Bender A, Pringle JR. Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol Cell Biol 1991, 11:1295-1305. 369400, 1996092.
    • (1991) Mol Cell Biol , vol.11 , pp. 1295-1305
    • Bender, A.1    Pringle, J.R.2
  • 24
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • 10.1126/science.1087447, 12934013
    • Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255. 10.1126/science.1087447, 12934013.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 25
    • 34249697574 scopus 로고    scopus 로고
    • Approaches for extracting practical information from gene co-expression networks in plant biology
    • 10.1093/pcp/pcm013, 17251202
    • Aoki K, Ogata Y, Shibata D. Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 2007, 48:381-390. 10.1093/pcp/pcm013, 17251202.
    • (2007) Plant Cell Physiol , vol.48 , pp. 381-390
    • Aoki, K.1    Ogata, Y.2    Shibata, D.3
  • 26
    • 38049079362 scopus 로고    scopus 로고
    • Protein-protein interaction networks and biology-what's the connection?
    • 10.1038/nbt0108-69, 18183023
    • Hakes L, Pinney JW, Robertson DL, Lovell SC. Protein-protein interaction networks and biology-what's the connection?. Nat Biotechnol 2008, 26:69-72. 10.1038/nbt0108-69, 18183023.
    • (2008) Nat Biotechnol , vol.26 , pp. 69-72
    • Hakes, L.1    Pinney, J.W.2    Robertson, D.L.3    Lovell, S.C.4
  • 27
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • 10.1038/47056, 10573422
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402:86-90. 10.1038/47056, 10573422.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 28
    • 0033055062 scopus 로고    scopus 로고
    • The use of gene clusters to infer functional coupling
    • 10.1073/pnas.96.6.2896, 15866, 10077608
    • Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 1999, 96:2896-2901. 10.1073/pnas.96.6.2896, 15866, 10077608.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 2896-2901
    • Overbeek, R.1    Fonstein, M.2    D'Souza, M.3    Pusch, G.D.4    Maltsev, N.5
  • 29
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
    • 10.1073/pnas.96.8.4285, 16324, 10200254
    • Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96:4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 4285-4288
    • Pellegrini, M.1    Marcotte, E.M.2    Thompson, M.J.3    Eisenberg, D.4    Yeates, T.O.5
  • 30
    • 0037197886 scopus 로고    scopus 로고
    • The identification of functional modules from the genomic association of genes
    • 10.1073/pnas.092632599, 122872, 11983890
    • Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 2002, 99:5890-5895. 10.1073/pnas.092632599, 122872, 11983890.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5890-5895
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 31
    • 18244386245 scopus 로고    scopus 로고
    • Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons
    • 10.1093/nar/gki545, 1088069, 15867197
    • Janga SC, Collado-Vides J, Moreno-Hagelsieb G. Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res 2005, 33:2521-2530. 10.1093/nar/gki545, 1088069, 15867197.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2521-2530
    • Janga, S.C.1    Collado-Vides, J.2    Moreno-Hagelsieb, G.3
  • 32
    • 79953032790 scopus 로고    scopus 로고
    • A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny
    • 10.1371/journal.pone.0017906, 3063783, 21455299
    • Wang Z, Zhang XC, Le MH, Xu D, Stacey G, Cheng J. A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One 2011, 6:e17906. 10.1371/journal.pone.0017906, 3063783, 21455299.
    • (2011) PLoS One , vol.6
    • Wang, Z.1    Zhang, X.C.2    Le, M.H.3    Xu, D.4    Stacey, G.5    Cheng, J.6
  • 34
    • 0034887573 scopus 로고    scopus 로고
    • Scale-free behavior in protein domain networks
    • 10.1093/oxfordjournals.molbev.a003957, 11504849
    • Wuchty S. Scale-free behavior in protein domain networks. Mol Biol Evol 2001, 18:1694-1702. 10.1093/oxfordjournals.molbev.a003957, 11504849.
    • (2001) Mol Biol Evol , vol.18 , pp. 1694-1702
    • Wuchty, S.1
  • 35
    • 33646001426 scopus 로고    scopus 로고
    • Graph theoretical insights into evolution of multidomain proteins
    • 10.1089/cmb.2006.13.351, 1815482, 16597245
    • Przytycka T, Davis G, Song N, Durand D. Graph theoretical insights into evolution of multidomain proteins. J Comput Biol 2006, 13:351-363. 10.1089/cmb.2006.13.351, 1815482, 16597245.
    • (2006) J Comput Biol , vol.13 , pp. 351-363
    • Przytycka, T.1    Davis, G.2    Song, N.3    Durand, D.4
  • 36
    • 34447506247 scopus 로고    scopus 로고
    • Comprehensive analysis of co-occurring domain sets in yeast proteins
    • 10.1186/1471-2164-8-161, 1919370, 17562021
    • Cohen-Gihon I, Nussinov R, Sharan R. Comprehensive analysis of co-occurring domain sets in yeast proteins. BMC Genomics 2007, 8:161. 10.1186/1471-2164-8-161, 1919370, 17562021.
    • (2007) BMC Genomics , vol.8 , pp. 161
    • Cohen-Gihon, I.1    Nussinov, R.2    Sharan, R.3
  • 40
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • 3245120, 22102590, The UniProt Consortium
    • The UniProt Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-D75. 3245120, 22102590, The UniProt Consortium.
    • (2012) Nucleic Acids Res , vol.40
  • 42
    • 34147120474 scopus 로고
    • A note on two problems in connexion with graphs
    • Dijkstra EW. A note on two problems in connexion with graphs. Numer Math 1959, 1:269-271.
    • (1959) Numer Math , vol.1 , pp. 269-271
    • Dijkstra, E.W.1
  • 43
    • 1542286754 scopus 로고    scopus 로고
    • Comparative analysis of protein domain organization
    • 10.1101/gr.1610504, 535408, 14993202
    • Ye Y, Godzik A. Comparative analysis of protein domain organization. Genome Res 2004, 14:343-353. 10.1101/gr.1610504, 535408, 14993202.
    • (2004) Genome Res , vol.14 , pp. 343-353
    • Ye, Y.1    Godzik, A.2
  • 44
    • 12344261833 scopus 로고    scopus 로고
    • The relationship between domain duplication and recombination
    • 10.1016/j.jmb.2004.11.050, 15663950
    • Vogel C, Teichmann SA, Pereira-Leal J. The relationship between domain duplication and recombination. J Mol Biol 2005, 346:355-365. 10.1016/j.jmb.2004.11.050, 15663950.
    • (2005) J Mol Biol , vol.346 , pp. 355-365
    • Vogel, C.1    Teichmann, S.A.2    Pereira-Leal, J.3
  • 45
    • 67849104643 scopus 로고    scopus 로고
    • G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery
    • 10.1093/nar/gkp463, 2703883, 19491312
    • Du Z, Li L, Chen CF, Yu PS, Wang JZ. G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res 2009, 37:W345-W349. 10.1093/nar/gkp463, 2703883, 19491312.
    • (2009) Nucleic Acids Res , vol.37
    • Du, Z.1    Li, L.2    Chen, C.F.3    Yu, P.S.4    Wang, J.Z.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.