메뉴 건너뛰기




Volumn 6577 LNBI, Issue , 2011, Pages 54-68

Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION REACTIONS; GENES; MOLECULAR BIOLOGY; PROTEINS; TOPOLOGY; WEB SERVICES;

EID: 79953174587     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-20036-6_7     Document Type: Conference Paper
Times cited : (6)

References (50)
  • 1
    • 3042841887 scopus 로고    scopus 로고
    • From syndrome families to functional genomics
    • Brunner, H.G., van Driel, M.A.: From syndrome families to functional genomics. Nat. Rev. Genet. 5(7), 545–551 (2004)
    • (2004) Nat. Rev. Genet. , vol.5 , Issue.7 , pp. 545-551
    • Brunner, H.G.1    Van Driel, M.A.2
  • 2
    • 0037146578 scopus 로고    scopus 로고
    • Finding Genes That Underlie Complex Traits
    • Glazier, A.M., Nadeau, J.H., Aitman, T.J.: Finding Genes That Underlie Complex Traits. Science 298(5602), 2345–2349 (2002)
    • (2002) Science , vol.298 , Issue.5602 , pp. 2345-2349
    • Glazier, A.M.1    Nadeau, J.H.2    Aitman, T.J.3
  • 4
    • 58149330480 scopus 로고    scopus 로고
    • Using gene expression to investigate the genetic basis of complex disorders
    • Nica, A.C., Dermitzakis, E.T.: Using gene expression to investigate the genetic basis of complex disorders. Human Molecular Genetics (2008)
    • (2008) Human Molecular Genetics
    • Nica, A.C.1    Dermitzakis, E.T.2
  • 5
    • 33645104470 scopus 로고    scopus 로고
    • SUSPECTS: Enabling fast and effective prioritization of positional candidates
    • Adie, E., Adams, R., Evans, K., Porteous, D., Pickard, B.: SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics 22(6), 773–774 (2006)
    • (2006) Bioinformatics , vol.22 , Issue.6 , pp. 773-774
    • Adie, E.1    Adams, R.2    Evans, K.3    Porteous, D.4    Pickard, B.5
  • 6
  • 7
    • 1542787787 scopus 로고    scopus 로고
    • Pocus: Mining genomic sequence annotation to predict disease genes
    • Turner, F., Clutterbuck, D., Semple, C.: Pocus: mining genomic sequence annotation to predict disease genes. Genome Biology 4(11), R75 (2003)
    • (2003) Genome Biology , vol.4 , Issue.11 , pp. R75
    • Turner, F.1    Clutterbuck, D.2    Semple, C.3
  • 8
    • 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., Figeys, D.: Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology 3 (2007)
    • (2007) Molecular Systems Biology , vol.3
    • Ewing, R.M.1    Chu, P.2    Elisma, F.3    Li, H.4    Figeys, D.5
  • 9
    • 77951952127 scopus 로고    scopus 로고
    • The power of protein interaction networks for associating genes with diseases
    • Navlakha, S., Kingsford, C.: The power of protein interaction networks for associating genes with diseases. Bioinformatics 26(8), 1057–1063 (2010)
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 1057-1063
    • Navlakha, S.1    Kingsford, C.2
  • 10
    • 33646884801 scopus 로고    scopus 로고
    • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
    • Franke, L., Bakel, H., Fokkens, L., de Jong, E.D., Egmont-Petersen, M., Wijmenga, C.: Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78(6), 1011–1025 (2006)
    • (2006) Am. J. Hum. Genet. , vol.78 , Issue.6 , pp. 1011-1025
    • Franke, L.1    Bakel, H.2    Fokkens, L.3    De Jong, E.D.4    Egmont-Petersen, M.5    Wijmenga, C.6
  • 11
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker, T., Sharan, R.: Protein networks in disease. Genome Research 18(4), 644–652 (2008)
    • (2008) Genome Research , vol.18 , Issue.4 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 12
    • 59649125020 scopus 로고    scopus 로고
    • A network-based method for predicting disease-causing genes
    • Karni, S., Soreq, H., Sharan, R.: A network-based method for predicting disease-causing genes. Journal of Computational Biology 16(2), 181–189 (2009)
    • (2009) Journal of Computational Biology , vol.16 , Issue.2 , pp. 181-189
    • Karni, S.1    Soreq, H.2    Sharan, R.3
  • 13
    • 33747035889 scopus 로고    scopus 로고
    • Predicting disease genes using protein-protein interactions
    • Oti, M., Snel, B., Huynen, M.A., Brunner, H.G.: Predicting disease genes using protein-protein interactions. J. Med. Genet., jmg.2006.041376 (2006)
    • (2006) J. Med. Genet., Jmg. , vol.41376 , Issue.2006
    • Oti, M.1    Snel, B.2    Huynen, M.A.3    Brunner, H.G.4
  • 14
    • 62849126285 scopus 로고    scopus 로고
    • Disease candidate gene identification and prioritization using protein interaction networks
    • Chen, J., Aronow, B., Jegga, A.: Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10(1), 73 (2009)
    • (2009) BMC Bioinformatics , vol.10 , Issue.1 , pp. 73
    • Chen, J.1    Aronow, B.2    Jegga, A.3
  • 15
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Köhler, S., Bauer, S., Horn, D., Robinson, P.N.: Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet. 82(4), 949–958 (2008)
    • (2008) Am. J. Hum. Genet. , vol.82 , Issue.4 , pp. 949-958
    • Köhler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 16
    • 76749134818 scopus 로고    scopus 로고
    • Associating genes and protein complexes with disease via network propagation
    • Vanunu, O., Magger, O., Ruppin, E., Shlomi, T., Sharan, R.: Associating genes and protein complexes with disease via network propagation. PLoS Comp. Bio. 6(1) (January 2010)
    • (2010) Plos Comp. Bio. , vol.6 , Issue.1
    • Vanunu, O.1    Magger, O.2    Ruppin, E.3    Shlomi, T.4    Sharan, R.5
  • 17
    • 77952877852 scopus 로고    scopus 로고
    • Predicting disease-related genes by topological similarity in human protein-protein interaction network
    • Zhang, L., Hu, K., Tang, Y.: Predicting disease-related genes by topological similarity in human protein-protein interaction network. Central European Journal of Physics 8, 672–682 (2010), 10.2478/s11534-009-0114-9
    • (2010) Central European Journal of Physics , vol.8 , pp. 672-682
    • Zhang, L.1    Hu, K.2    Tang, Y.3
  • 21
    • 20044396570 scopus 로고    scopus 로고
    • Integrative analysis of the cancer transcriptome
    • Rhodes, D.R., Chinnaiyan, A.M.: Integrative analysis of the cancer transcriptome. Nat. Genet. 2005)
    • (2005) Nat. Genet
    • Rhodes, D.R.1    Chinnaiyan, A.M.2
  • 22
    • 75149137951 scopus 로고    scopus 로고
    • Functional characterization and topological modularity of molecular interaction networks
    • Pandey, J., Koyutürk, M., Grama, A.: Functional characterization and topological modularity of molecular interaction networks. BMC Bioinformatics 11(Suppl. 1), S35 (2010)
    • (2010) BMC Bioinformatics , vol.11 , pp. S35
    • Pandey, J.1    Koyutürk, M.2    Grama, A.3
  • 23
    • 78649944559 scopus 로고    scopus 로고
    • Petals: Proteomic evaluation and topological analysis of a mutated locus signaling
    • Bebek, G., Patel, V., Chance, M.R.: Petals: Proteomic evaluation and topological analysis of a mutated locus signaling. BMC Bioinformatics 11, 596 (2010)
    • (2010) BMC Bioinformatics , vol.11 , pp. 596
    • Bebek, G.1    Patel, V.2    Chance, M.R.3
  • 25
    • 36849004088 scopus 로고    scopus 로고
    • Pathfinder: Mining signal transduction pathway segments from protein-protein interaction networks
    • Bebek, G., Yang, J.: Pathfinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics 8, 335 (2007)
    • (2007) BMC Bioinformatics , vol.8 , pp. 335
    • Bebek, G.1    Yang, J.2
  • 26
    • 54349104506 scopus 로고    scopus 로고
    • Netgrep: Fast network schema searches in interactomes
    • Banks, E., Nabieva, E., Peterson, R., Singh, M.: Netgrep: fast network schema searches in interactomes. Genome Biology 9(9) (2008)
    • (2008) Genome Biology , vol.9 , Issue.9
    • Banks, E.1    Nabieva, E.2    Peterson, R.3    Singh, M.4
  • 27
    • 47249152384 scopus 로고    scopus 로고
    • Protein function prediction based on patterns in biological networks
    • Vingron, M., Wong, L. (eds.), Springer, Heidelberg
    • Kirac, M., Özsoyoģlu, G.: Protein function prediction based on patterns in biological networks. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 197–213. Springer, Heidelberg (2008)
    • (2008) RECOMB 2008. LNCS (LNBI) , vol.4955 , pp. 197-213
    • Kirac, M.1    Özsoyoģlu, G.2
  • 28
    • 33749993417 scopus 로고    scopus 로고
    • The consensus coding sequences of human breast and colorectal cancers
    • Sjöblom, T., Jones, S., Wood, L.D., Parsons, D.W., Lin, J., Barber, T.D., et al.: The consensus coding sequences of human breast and colorectal cancers. Science 314(5797), 268–274 (2006)
    • (2006) Science , vol.314 , Issue.5797 , pp. 268-274
    • Sjöblom, T.1    Jones, S.2    Wood, L.D.3    Parsons, D.W.4    Lin, J.5    Barber, T.D.6
  • 29
    • 36248962105 scopus 로고    scopus 로고
    • The genomic landscapes of human breast and colorectal cancers
    • Wood, L.D., Parsons, D.W., Jones, S., Lin, J., Sjöblom, T., Leary, R.J.: The genomic landscapes of human breast and colorectal cancers. Science 318(5853), 1108–1113 (2007)
    • (2007) Science , vol.318 , Issue.5853 , pp. 1108-1113
    • Wood, L.D.1    Parsons, D.W.2    Jones, S.3    Lin, J.4    Sjöblom, T.5    Leary, R.J.6
  • 30
    • 56749183466 scopus 로고    scopus 로고
    • Epithelial pten is dispensable for intestinal homeostasis but suppresses adenoma development and progression after apc mutation
    • Marsh, V., Winton, D.J., Williams, G.T., Dubois, N., Trumpp, A., Sansom, O.J., Clarke, A.R.: Epithelial pten is dispensable for intestinal homeostasis but suppresses adenoma development and progression after apc mutation. Nat. Genet. 40(12), 1436–1444 (2008)
    • (2008) Nat. Genet. , vol.40 , Issue.12 , pp. 1436-1444
    • Marsh, V.1    Winton, D.J.2    Williams, G.T.3    Dubois, N.4    Trumpp, A.5    Sansom, O.J.6    Clarke, A.R.7
  • 31
    • 56049110529 scopus 로고    scopus 로고
    • The pleiotropic phenotype of apc mutations in the mouse: Allele specificity and effects of the genetic background
    • Halberg, R.B., Chen, X., Amos-Landgraf, J.M., White, A., Rasmussen, K., Clipson, L., et al.: The pleiotropic phenotype of apc mutations in the mouse: allele specificity and effects of the genetic background. Genetics 180(1), 601–609 (2008)
    • (2008) Genetics , vol.180 , Issue.1 , pp. 601-609
    • Halberg, R.B.1    Chen, X.2    Amos-Landgraf, J.M.3    White, A.4    Rasmussen, K.5    Clipson, L.6
  • 33
    • 77952307412 scopus 로고    scopus 로고
    • Role of centrality in network-based prioritization of disease genes
    • Pizzuti, C., Ritchie, M.D., Giacobini, M. (eds.), Springer, Heidelberg
    • Erten, S., Koyutürk, M.: Role of centrality in network-based prioritization of disease genes. In: Pizzuti, C., Ritchie, M.D., Giacobini, M. (eds.) EvoBIO 2010. LNCS, vol. 6023, pp. 13– 25. Springer, Heidelberg (2010)
    • (2010) Evobio 2010. LNCS , vol.6023 , pp. 13-25
    • Erten, S.1    Koyutürk, M.2
  • 35
    • 44349113144 scopus 로고    scopus 로고
    • Estimating the size of the human interactome
    • Stumpf, M.P.H., Thorne, T., de Silva, E., et al.: Estimating the size of the human interactome. Proc. Natl. Acad. Sci. USA 105(19), 6959–6964 (2008)
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , Issue.19 , pp. 6959-6964
    • Stumpf, M.P.H.1    Thorne, T.2    De Silva, E.3
  • 36
    • 13844314048 scopus 로고    scopus 로고
    • Conserved patterns of protein interaction in multiple species
    • Sharan, R., Suthram, S., et al.: Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102(6), 1974–1979 (2005)
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.6 , pp. 1974-1979
    • Sharan, R.1    Suthram, S.2
  • 37
    • 33747586075 scopus 로고    scopus 로고
    • A direct comparison of protein interaction confidence assignment schemes
    • Suthram, S., Shlomi, T., Ruppin, E., Sharan, R., Ideker, T.: A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics 7, 360+ (2006)
    • (2006) BMC Bioinformatics , vol.7 , pp. 360+
    • Suthram, S.1    Shlomi, T.2    Ruppin, E.3    Sharan, R.4    Ideker, T.5
  • 38
    • 0032893083 scopus 로고    scopus 로고
    • Kaps, et al.: Mips: A database for genomes and protein sequences. Nuc. Ac
    • Mewes, H.W., Heumann, K., Kaps, et al.: Mips: a database for genomes and protein sequences. Nuc. Ac. Res. 27(1), 44–48 (1999)
    • (1999) Res , vol.27 , Issue.1 , pp. 44-48
    • Mewes, H.W.1    Heumann, K.2
  • 40
    • 58149182724 scopus 로고    scopus 로고
    • Ncbi geo: Archive for high-throughput functional genomic data
    • Barrett, T., Troup, D.B., et al.: Ncbi geo: archive for high-throughput functional genomic data. Nucleic Acids Res. 37(Database issue), 885–890 (2009)
    • (2009) Nucleic Acids Res , vol.37 , pp. 885-890
    • Barrett, T.1    Troup, D.B.2
  • 42
    • 0037447257 scopus 로고    scopus 로고
    • Assessing experimentally derived interactions in a small world
    • Goldberg, D.S., Roth, F.P.: Assessing experimentally derived interactions in a small world. Proc. Natl. Acad. Sci. USA 100(8), 4372–4376 (2003)
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.8 , pp. 4372-4376
    • Goldberg, D.S.1    Roth, F.P.2
  • 43
    • 57049148610 scopus 로고    scopus 로고
    • Graph sparsification by effective resistances
    • Spielman, D.A., Srivastava, N.: Graph sparsification by effective resistances. In: STOC, pp. 563–568 (2008)
    • (2008) STOC , pp. 563-568
    • Spielman, D.A.1    Srivastava, N.2
  • 44
    • 0001418604 scopus 로고
    • Random walks and the effective resistance of networks
    • Tetali, P.: Random walks and the effective resistance of networks. Journal of Theoretical Probability 4(1), 101–109 (1991)
    • (1991) Journal of Theoretical Probability , vol.4 , Issue.1 , pp. 101-109
    • Tetali, P.1
  • 46
    • 41149096059 scopus 로고    scopus 로고
    • Random walk with restart: Fast solutions and applications
    • Tong, H., Faloutsos, C., Pan, J.Y.: Random walk with restart: fast solutions and applications. Knowledge and Information Systems 14(3), 327–346 (2008)
    • (2008) Knowledge and Information Systems , vol.14 , Issue.3 , pp. 327-346
    • Tong, H.1    Faloutsos, C.2    Pan, J.Y.3
  • 47
    • 70349754527 scopus 로고    scopus 로고
    • Rrw: Repeated random walks on genome-scale protein networks for local cluster discovery
    • Macropol, K., Can, T., Singh, A.: Rrw: repeated random walks on genome-scale protein networks for local cluster discovery. BMC Bioinformatics 10(1), 283 (2009)
    • (2009) BMC Bioinformatics , vol.10 , Issue.1 , pp. 283
    • Macropol, K.1    Can, T.2    Singh, A.3
  • 48
    • 33749577591 scopus 로고    scopus 로고
    • Center-piece subgraphs: Problem definition and fast solutions
    • ACM, NY
    • Tong, H., Faloutsos, C.: Center-piece subgraphs: problem definition and fast solutions. In: KDD 2006: Proceedings of the 12th ACM SIGKDD, pp. 404–413. ACM, NY (2006)
    • (2006) KDD 2006: Proceedings of the 12Th ACM SIGKDD , pp. 404-413
    • Tong, H.1    Faloutsos, C.2
  • 49
    • 33846056843 scopus 로고    scopus 로고
    • Entrez Gene: Gene-centered information at NCBI. Nucl
    • Maglott, D., Ostell, J., Pruitt, K.D., Tatusova, T.: Entrez Gene: gene-centered information at NCBI. Nucl. Acids Res. 35(suppl-1), D26–D31 (2007)
    • (2007) Acids Res , vol.35 , pp. D26-D31
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.