메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages

Inferring protein function by domain context similarities in protein-protein interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

GENOME SEQUENCING PROJECTS; INFORMATION RESOURCE; NOVEL PROTEINS; PREDICTION ACCURACY; PROTEIN DOMAINS; PROTEIN FUNCTIONS; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS;

EID: 72549092050     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-395     Document Type: Article
Times cited : (33)

References (28)
  • 1
    • 27644576841 scopus 로고    scopus 로고
    • High-throughput two-hybrid analysis. The promise and the peril
    • 10.1111/j.1742-4658.2005.04973.x, 16262681
    • Fields S. High-throughput two-hybrid analysis. The promise and the peril. FEBS J 2005, 272(21):5391-5399. 10.1111/j.1742-4658.2005.04973.x, 16262681.
    • (2005) FEBS J , vol.272 , Issue.21 , pp. 5391-5399
    • Fields, S.1
  • 2
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • 10.1038/nature01511, 12634793
    • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003, 422(6928):198-207. 10.1038/nature01511, 12634793.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 3
    • 23844447959 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • 10.1089/cmb.2005.12.835, 16108720
    • Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 2005, 12(6):835-846. 10.1089/cmb.2005.12.835, 16108720.
    • (2005) J Comput Biol , vol.12 , Issue.6 , pp. 835-846
    • Sharan, R.1    Ideker, T.2    Kelley, B.3    Shamir, R.4    Karp, R.M.5
  • 4
    • 0742304254 scopus 로고    scopus 로고
    • Prediction of protein function using protein-protein interaction data
    • Deng M, Zhang K, Mehta S, Chen T, Sun F. Prediction of protein function using protein-protein interaction data. J ComputBiol 2003, 10(6):947-960.
    • (2003) J ComputBiol , vol.10 , Issue.6 , pp. 947-960
    • Deng, M.1    Zhang, K.2    Mehta, S.3    Chen, T.4    Sun, F.5
  • 5
    • 1542271409 scopus 로고    scopus 로고
    • Predicting protein function from protein/protein interaction data: a probabilistic approach
    • 10.1093/bioinformatics/btg1026, 12855458
    • Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 2003, 19(Suppl 1):i197-204. 10.1093/bioinformatics/btg1026, 12855458.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL 1
    • Letovsky, S.1    Kasif, S.2
  • 6
    • 1542327694 scopus 로고    scopus 로고
    • Whole-genome annotation by using evidence integration in functional-linkage networks
    • 10.1073/pnas.0307326101, 365715, 14981259
    • Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci USA 2004, 101(9):2888-2893. 10.1073/pnas.0307326101, 365715, 14981259.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.9 , pp. 2888-2893
    • Karaoz, U.1    Murali, T.M.2    Letovsky, S.3    Zheng, Y.4    Ding, C.5    Cantor, C.R.6    Kasif, S.7
  • 7
    • 29144442904 scopus 로고    scopus 로고
    • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
    • 10.1093/bioinformatics/bti1054, 15961472
    • Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 2005, 21(Suppl 1):i302-310. 10.1093/bioinformatics/bti1054, 15961472.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL 1
    • Nabieva, E.1    Jim, K.2    Agarwal, A.3    Chazelle, B.4    Singh, M.5
  • 8
    • 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(12):1257-1261. 10.1038/82360, 11101803.
    • (2000) Nat Biotechnol , vol.18 , Issue.12 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 9
    • 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(6):523-531. 10.1002/yea.706, 11284008.
    • (2001) Yeast , vol.18 , Issue.6 , pp. 523-531
    • Hishigaki, H.1    Nakai, K.2    Ono, T.3    Tanigami, A.4    Takagi, T.5
  • 10
    • 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(13):1623-1630. 10.1093/bioinformatics/btl145, 16632496.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.K.2    Wong, L.3
  • 11
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • 10.1038/nbt825, 12740586
    • Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003, 21(6):697-700. 10.1038/nbt825, 12740586.
    • (2003) Nat Biotechnol , vol.21 , Issue.6 , pp. 697-700
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 12
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • 10.1186/1471-2105-7-207, 1473204, 16613608
    • 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 Bioinformatics 2006, 7:207. 10.1186/1471-2105-7-207, 1473204, 16613608.
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 13
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • 10.1186/1471-2105-4-2, 149346, 12525261
    • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 14
    • 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(3):1128-1133. 10.1073/pnas.0237338100, 298738, 12538875.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.3 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 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(21):12123-12128. 10.1073/pnas.2032324100, 218723, 14517352.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.21 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 16
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
    • 10.1038/ng776, 11694880
    • Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29(4):482-486. 10.1038/ng776, 11694880.
    • (2001) Nat Genet , vol.29 , Issue.4 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 17
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl 1):S233-240.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 18
    • 0038014879 scopus 로고    scopus 로고
    • Co-clustering of biological networks and gene expression data
    • Hanisch D, Zien A, Zimmer R, Lengauer T. Co-clustering of biological networks and gene expression data. Bioinformatics 2002, 18(Suppl 1):S145-154.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL 1
    • Hanisch, D.1    Zien, A.2    Zimmer, R.3    Lengauer, T.4
  • 19
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    • 10.1093/nar/30.1.303, 99070, 11752321
    • Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30(1):303-305. 10.1093/nar/30.1.303, 99070, 11752321.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.M.5    Eisenberg, D.6
  • 21
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: a comprehensive database of protein domain families based on seed alignments
    • 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L, 9223186
    • Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997, 28(3):405-420. 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L, 9223186.
    • (1997) Proteins , vol.28 , Issue.3 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 23
    • 1542346418 scopus 로고    scopus 로고
    • A novel method for protein secondary structure prediction using dual-layer SVM and profiles
    • 10.1002/prot.10634, 14997569
    • Guo J, Chen H, Sun Z, Lin Y. A novel method for protein secondary structure prediction using dual-layer SVM and profiles. Proteins 2004, 54(4):738-743. 10.1002/prot.10634, 14997569.
    • (2004) Proteins , vol.54 , Issue.4 , pp. 738-743
    • Guo, J.1    Chen, H.2    Sun, Z.3    Lin, Y.4
  • 24
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach
    • 10.1006/jmbi.2001.4580, 11327775
    • Hua S, Sun Z. A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. J Mol Biol 2001, 308(2):397-407. 10.1006/jmbi.2001.4580, 11327775.
    • (2001) J Mol Biol , vol.308 , Issue.2 , pp. 397-407
    • Hua, S.1    Sun, Z.2
  • 25
    • 2342435295 scopus 로고    scopus 로고
    • Mapping Gene Ontology to proteins based on protein-protein interaction data
    • 10.1093/bioinformatics/btg500, 14751964
    • Deng M, Tu Z, Sun F, Chen T. Mapping Gene Ontology to proteins based on protein-protein interaction data. Bioinformatics 2004, 20(6):895-902. 10.1093/bioinformatics/btg500, 14751964.
    • (2004) Bioinformatics , vol.20 , Issue.6 , pp. 895-902
    • Deng, M.1    Tu, Z.2    Sun, F.3    Chen, T.4
  • 26
    • 34548084807 scopus 로고    scopus 로고
    • Inferring protein domain interactions from databases of interacting proteins
    • 10.1186/gb-2005-6-10-r89, 1257472, 16207360
    • Riley R, Lee C, Sabatti C, Eisenberg D. Inferring protein domain interactions from databases of interacting proteins. Genome Biol 2005, 6(10):R89. 10.1186/gb-2005-6-10-r89, 1257472, 16207360.
    • (2005) Genome Biol , vol.6 , Issue.10
    • Riley, R.1    Lee, C.2    Sabatti, C.3    Eisenberg, D.4
  • 27
    • 33645818955 scopus 로고    scopus 로고
    • The DIMA web resource--exploring the protein domain network
    • 10.1093/bioinformatics/btl050, 16481337
    • Pagel P, Oesterheld M, Stumpflen V, Frishman D. The DIMA web resource--exploring the protein domain network. Bioinformatics 2006, 22(8):997-998. 10.1093/bioinformatics/btl050, 16481337.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 997-998
    • Pagel, P.1    Oesterheld, M.2    Stumpflen, V.3    Frishman, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.