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Volumn 781, Issue , 2011, Pages 399-414

Predicting Node Characteristics from Molecular Networks

Author keywords

Functional linkage networks; Gene function prediction; Label propagation

Indexed keywords

ALGORITHM; FUNCTIONAL LINK ARTIFICIAL NEURAL NETWORK; GENE FUNCTION; NEIGHBORHOOD; PREDICTION; ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; METABOLISM; METHODOLOGY; PREDICTIVE VALUE; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION;

EID: 80054775533     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-276-2_20     Document Type: Chapter
Times cited : (2)

References (52)
  • 1
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte, E.M., et al., Detecting protein function and protein-protein interactions from genome sequences. Science, 1999. 285(5428): p. 751–3.
    • (1999) Science , vol.285 , Issue.5428 , pp. 751-753
    • Marcotte, E.M.1
  • 2
    • 43249114206 scopus 로고    scopus 로고
    • Network-based global inference of human disease genes
    • Wu, X., et al., Network-based global inference of human disease genes. Mol Syst Biol, 2008. 4: p. 189.
    • (2008) Mol Syst Biol , vol.4 , pp. 189
    • Wu, X.1
  • 3
    • 33646568805 scopus 로고    scopus 로고
    • Gene prioritization through genomic data fusion
    • Aerts, S., et al., Gene prioritization through genomic data fusion. Nat Biotechnol, 2006. 24(5): p. 537–44.
    • (2006) Nat Biotechnol , vol.24 , Issue.5 , pp. 537-544
    • Aerts, S.1
  • 4
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan, R., I. Ulitsky, and R. Shamir, Network-based prediction of protein function. Mol Syst Biol, 2007. 3: p. 88.
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 5
    • 33845545435 scopus 로고    scopus 로고
    • The modular nature of genetic diseases
    • Oti, M. and H.G. Brunner, The modular nature of genetic diseases. Clin Genet, 2007. 71(1): p. 1–11.
    • (2007) Clin Genet , vol.71 , Issue.1 , pp. 1-11
    • Oti, M.1    Brunner, H.G.2
  • 6
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M., et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000. 25(1): p. 25–9.
    • (2000) Nat Genet , vol.25 , Issue.1 , pp. 25-29
    • Ashburner, M.1
  • 7
    • 0032919364 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Ogata, H., et al., KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res, 1999. 27(1): p. 29–34.
    • (1999) Nucleic Acids Res , vol.27 , Issue.1 , pp. 29-34
    • Ogata, H.1
  • 8
    • 9144257282 scopus 로고    scopus 로고
    • The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
    • Ruepp, A., et al., The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res, 2004. 32(18): p. 5539–45.
    • (2004) Nucleic Acids Res , vol.32 , Issue.18 , pp. 5539-5545
    • Ruepp, A.1
  • 9
    • 84954358609 scopus 로고    scopus 로고
    • The Human Phenotype Ontology: A tool for annotating and analyzing human hereditary disease
    • Robinson, P.N., et al., The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet, 2008. 83(5): p. 610–5.
    • (2008) Am J Hum Genet , vol.83 , Issue.5 , pp. 610-615
    • Robinson, P.N.1
  • 10
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh, A., et al., Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res, 2005. 33(Database issue): p. D514–7.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database , pp. D514-D517
    • Hamosh, A.1
  • 11
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • Chua, H.N., W.K. Sung, and L. Wong, Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 2006. 22(13): p. 1623–30.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.K.2    Wong, L.3
  • 12
    • 0036790999 scopus 로고    scopus 로고
    • Transitive functional annotation by shortest-path analysis of gene expression data
    • Zhou, X., M.C. Kao, and W.H. Wong, Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci USA, 2002. 99(20): p. 12783–8.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.20 , pp. 12783-12788
    • Zhou, X.1    Kao, M.C.2    Wong, W.H.3
  • 13
    • 33745113181 scopus 로고    scopus 로고
    • Discovery of biological networks from diverse functional genomic data
    • Myers, C.L., et al., Discovery of biological networks from diverse functional genomic data. Genome Biol, 2005. 6(13): p. R114.
    • (2005) Genome Biol , vol.6 , Issue.13 , pp. p. R114
    • Myers, C.L.1
  • 14
    • 0036668351 scopus 로고    scopus 로고
    • Protective role of melatonin and a combination of vitamin C and vitamin E on lung toxicity induced by chlorpyrifos-ethyl in rats
    • Karaoz, E., et al., Protective role of melatonin and a combination of vitamin C and vitamin E on lung toxicity induced by chlorpyrifos-ethyl in rats. Exp Toxicol Pathol, 2002. 54(2): p. 97–108.
    • (2002) Exp Toxicol Pathol , vol.54 , Issue.2 , pp. 97-108
    • Karaoz, E.1
  • 15
    • 0742304254 scopus 로고    scopus 로고
    • Prediction of protein function using protein-protein interaction data
    • Deng, M., et al., Prediction of protein function using protein-protein interaction data. J Comput Biol, 2003. 10(6): p. 947–60.
    • (2003) J Comput Biol , vol.10 , Issue.6 , pp. 947-960
    • Deng, M.1
  • 16
    • 29144442904 scopus 로고    scopus 로고
    • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
    • Suppl 1: p
    • Nabieva, E., et al., Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics, 2005. 21 Suppl 1: p. i302–10.
    • (2005) Bioinformatics , vol.21 , pp. i302-i310
    • Nabieva, E.1
  • 17
    • 47549107689 scopus 로고    scopus 로고
    • GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function
    • Mostafavi, S., et al., GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol, 2008. 9 Suppl 1: p. S4.
    • (2008) Genome Biol , vol.9 , pp. S4
    • Mostafavi, S.1
  • 18
    • 27544435126 scopus 로고    scopus 로고
    • Fast protein classification with multiple networks
    • Tsuda, K., H. Shin, and B. Scholkopf, Fast protein classification with multiple networks. Bioinformatics, 2005. 21 Suppl 2: p. ii59-65.
    • (2005) Bioinformatics , vol.21 , pp. ii59-ii65
    • Tsuda, K.1    Shin, H.2    Scholkopf, B.3
  • 19
    • 33845701686 scopus 로고    scopus 로고
    • The art of gene function prediction
    • author reply 1475–6
    • Murali, T.M., C.J. Wu, and S. Kasif, The art of gene function prediction. Nat Biotechnol, 2006. 24(12): p. 1474–5; author reply 1475–6.
    • (2006) Nat Biotechnol , vol.24 , Issue.12 , pp. 1474-1475
    • Murali, T.M.1    Wu, C.J.2    Kasif, S.3
  • 20
    • 3142622851 scopus 로고    scopus 로고
    • An integrated probabilistic model for functional prediction of proteins
    • Deng, M., T. Chen, and F. Sun, An integrated probabilistic model for functional prediction of proteins. J Comput Biol, 2004. 11(2–3): p. 463–75.
    • (2004) J Comput Biol , vol.11 , Issue.2-3 , pp. 463-475
    • Deng, M.1    Chen, T.2    Sun, F.3
  • 21
    • 77954309042 scopus 로고    scopus 로고
    • Fast Integration of Heterogeneous Data Sources for Predicting Gene Function with Limited Annotation
    • Mostafavi, S. and Q. Morris, Fast Integration of Heterogeneous Data Sources for Predicting Gene Function with Limited Annotation. Bioinformatics, 2010.
    • (2010) Bioinformatics
    • Mostafavi, S.1    Morris, Q.2
  • 22
    • 8844263749 scopus 로고    scopus 로고
    • A statistical framework for genomic data fusion
    • Lanckriet, G.R., et al., A statistical framework for genomic data fusion. Bioinformatics, 2004. 20(16): p. 2626–35.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2626-2635
    • Lanckriet, G.R.1
  • 23
    • 47549116997 scopus 로고    scopus 로고
    • A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
    • Suppl 1: p. S2
    • Pena-Castillo, L., et al., A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol, 2008. 9 Suppl 1: p. S2.
    • (2008) Genome Biol , vol.9
    • Pena-Castillo, L.1
  • 24
    • 0036100116 scopus 로고    scopus 로고
    • Learning gene functional classifications from multiple data types
    • Pavlidis, P., et al., Learning gene functional classifications from multiple data types. J Comput Biol, 2002. 9(2): p. 401–11.
    • (2002) J Comput Biol , vol.9 , Issue.2 , pp. 401-411
    • Pavlidis, P.1
  • 25
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • Zhang, B. and S. Horvath, A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol, 2005. 4: p. Article17.
    • (2005) Stat Appl Genet Mol Biol , vol.4 , pp. 17
    • Zhang, B.1    Horvath, S.2
  • 26
    • 33745601692 scopus 로고    scopus 로고
    • Effective similarity measures for expression profiles
    • Yona, G., et al., Effective similarity measures for expression profiles. Bioinformatics, 2006. 22(13): p. 1616–22.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1616-1622
    • Yona, G.1
  • 27
    • 77954269901 scopus 로고    scopus 로고
    • The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function
    • Accepted(Webserver Issue
    • Warde-Farley, D., et al., The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res, 2010. Accepted(Webserver Issue).
    • (2010) Nucleic Acids Res
    • Warde-Farley, D.1
  • 28
    • 75649111192 scopus 로고    scopus 로고
    • The genetic landscape of a cell
    • Costanzo, M., et al., The genetic landscape of a cell. Science, 2010. 327(5964): p. 425–31.
    • (2010) Science , vol.327 , Issue.5964 , pp. 425-431
    • Costanzo, M.1
  • 29
    • 10744230485 scopus 로고    scopus 로고
    • Global mapping of the yeast genetic interaction network
    • Tong, A.H., et al., Global mapping of the yeast genetic interaction network. Science, 2004. 303(5659): p. 808–13.
    • (2004) Science , vol.303 , Issue.5659 , pp. 808-813
    • Tong, A.H.1
  • 30
    • 57449115862 scopus 로고    scopus 로고
    • Information-based methods for predicting gene function from systematic gene knock-downs
    • Weirauch, M.T., et al., Information-based methods for predicting gene function from systematic gene knock-downs. BMC Bioinformatics, 2008. 9: p. 463.
    • (2008) BMC Bioinformatics , vol.9
    • Weirauch, M.T.1
  • 31
    • 0035044077 scopus 로고    scopus 로고
    • Assessment of prediction accuracy of protein function from protein--protein interaction data
    • Hishigaki, H., et al., Assessment of prediction accuracy of protein function from protein--protein interaction data. Yeast, 2001. 18(6): p. 523–31.
    • (2001) Yeast , vol.18 , Issue.6 , pp. 523-531
    • Hishigaki, H.1
  • 32
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski, B., P. Uetz, and S. Fields, A network of protein-protein interactions in yeast. Nat Biotechnol, 2000. 18(12): p. 1257–61.
    • (2000) Nat Biotechnol , vol.18 , Issue.12 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 33
    • 22944492898 scopus 로고    scopus 로고
    • Learning with Local and Global Consistency
    • MIT Press: Vancouver, BC, Canada
    • Zhou, D., et al., Learning with Local and Global Consistency, in Neural Information Processing Systems. 2003, MIT Press: Vancouver, BC, Canada.
    • (2003) Neural Information Processing Systems
    • Zhou, D.1
  • 34
    • 2342475726 scopus 로고    scopus 로고
    • Protein ranking: From local to global structure in the protein similarity network
    • Weston, J., et al., Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci USA, 2004. 101(17): p. 6559–63.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.17 , pp. 6559-6563
    • Weston, J.1
  • 35
    • 75149153011 scopus 로고    scopus 로고
    • Predicting protein functions by relaxation labelling protein interaction network
    • Suppl 1: p. S64
    • Hu, P., H. Jiang, and A. Emili, Predicting protein functions by relaxation labelling protein interaction network. BMC Bioinformatics, 2010. 11 Suppl 1: p. S64.
    • (2010) BMC Bioinformatics , vol.11
    • Hu, P.1    Jiang, H.2    Emili, A.3
  • 38
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vazquez, A., et al., Global protein function prediction from protein-protein interaction networks. Nat Biotechnol, 2003. 21(6): p. 697–700.
    • (2003) Nat Biotechnol , vol.21 , Issue.6 , pp. 697-700
    • Vazquez, A.1
  • 39
    • 1542327694 scopus 로고    scopus 로고
    • Whole-genome annotation by using evidence integration in functional-linkage networks
    • Karaoz, U., et al., Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci USA, 2004. 101(9): p. 2888–93.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.9 , pp. 2888-2893
    • Karaoz, U.1
  • 40
    • 2642566695 scopus 로고    scopus 로고
    • A probabilistic view of gene function
    • Fraser, A.G. and E.M. Marcotte, A probabilistic view of gene function. Nat Genet, 2004. 36(6): p. 559–64.
    • (2004) Nat Genet , vol.36 , Issue.6 , pp. 559-564
    • Fraser, A.G.1    Marcotte, E.M.2
  • 41
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • Lee, I., et al., A probabilistic functional network of yeast genes. Science, 2004. 306(5701): p. 1555–8.
    • (2004) Science , vol.306 , Issue.5701 , pp. 1555-1558
    • Lee, I.1
  • 42
    • 34548749776 scopus 로고    scopus 로고
    • Context-sensitive data integration and prediction of biological networks
    • Myers, C.L. and O.G. Troyanskaya, Context-sensitive data integration and prediction of biological networks. Bioinformatics, 2007. 23(17): p. 2322–30.
    • (2007) Bioinformatics , vol.23 , Issue.17 , pp. 2322-2330
    • Myers, C.L.1    Troyanskaya, O.G.2
  • 43
    • 66449120271 scopus 로고    scopus 로고
    • Exploring the human genome with functional maps
    • Huttenhower, C., et al., Exploring the human genome with functional maps. Genome Res, 2009. 19(6): p. 1093–106.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1093-1106
    • Huttenhower, C.1
  • 45
    • 75949120438 scopus 로고    scopus 로고
    • How and when should interactome-derived clusters be used to predict functional modules and protein function?
    • Song, J. and M. Singh, How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics, 2009. 25(23): p. 3143–50.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3143-3150
    • Song, J.1    Singh, M.2
  • 46
    • 33748513704 scopus 로고    scopus 로고
    • Finding function: Evaluation methods for functional genomic data
    • Myers, C.L., et al., Finding function: evaluation methods for functional genomic data. BMC Genomics, 2006. 7: p. 187.
    • (2006) BMC Genomics , vol.7
    • Myers, C.L.1
  • 48
    • 33750975917 scopus 로고    scopus 로고
    • Support vector machine learning from heterogeneous data: An empirical analysis using protein sequence and structure
    • Lewis, D.P., T. Jebara, and W.S. Noble, Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinformatics, 2006. 22(22): p. 2753–60.
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2753-2760
    • Lewis, D.P.1    Jebara, T.2    Noble, W.S.3
  • 50
    • 65349085291 scopus 로고    scopus 로고
    • Global networks of functional coupling in eukaryotes from comprehensive data integration
    • Alexeyenko, A. and E.L. Sonnhammer, Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res, 2009. 19(6): p. 1107–16.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1107-1116
    • Alexeyenko, A.1    Sonnhammer, E.L.2
  • 51
    • 13444249988 scopus 로고    scopus 로고
    • STRING: Known and predicted protein-protein associations, integrated and transferred across organisms
    • von Mering, C., et al., STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res, 2005. 33(Database issue): p. D433–7.
    • (2005) Nucleic Acids Res , vol.33 , Issue.Database , pp. D433-D437
    • von Mering, C.1
  • 52
    • 52949087576 scopus 로고    scopus 로고
    • A genomewide functional network for the laboratory mouse
    • Guan, Y., et al., A genomewide functional network for the laboratory mouse. PLoS Comput Biol, 2008. 4(9): p. e1000165.
    • (2008) Plos Comput Biol , vol.4 , Issue.9
    • Guan, Y.1


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