메뉴 건너뛰기




Volumn 18, Issue 3, 2011, Pages 379-390

Extracting between-pathway models from E-MAP interactions using expected graph compression

Author keywords

Algorithms; combinatorial optimization; functional genomics

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; CONFERENCE PAPER; FUNGAL GENE; GENE EXPRESSION REGULATION; GENETIC EPISTASIS; GENETICS; INFORMATION PROCESSING; METHODOLOGY; MOLECULAR GENETICS; SACCHAROMYCES CEREVISIAE;

EID: 79952422056     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0268     Document Type: Conference Paper
Times cited : (5)

References (26)
  • 2
    • 43249117094 scopus 로고    scopus 로고
    • Functional maps of protein complexes from quantitative genetic interaction data
    • Bandyopadhyay, S., Kelley, R., Krogan, N.J., et al. 2008. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput. Biol. 4, e1000065.
    • (2008) PLoS Comput. Biol. , vol.4
    • Bandyopadhyay, S.1    Kelley, R.2    Krogan, N.J.3
  • 3
    • 0347513219 scopus 로고    scopus 로고
    • Characterizing gene sets with FuncAssociate
    • DOI 10.1093/bioinformatics/btg363
    • Berriz, G., King, O., Bryant, B., et al. 2003. Characterizing gene sets with Func Associate. Bioinformatics 19, 2502-2504. (Pubitemid 38016661)
    • (2003) Bioinformatics , vol.19 , Issue.18 , pp. 2502-2504
    • Berriz, G.F.1    King, O.D.2    Bryant, B.3    Sander, C.4    Roth, F.P.5
  • 4
    • 65449186979 scopus 로고    scopus 로고
    • Fault tolerance in protein interaction networks: Stable bipartite subgraphs and redundant pathways
    • Brady, A., Maxwell, K., Daniels, N., et al. 2009. Fault tolerance in protein interaction networks: Stable bipartite subgraphs and redundant pathways. PLoS ONE 4, e5364.
    • (2009) PLoS ONE , vol.4
    • Brady, A.1    Maxwell, K.2    Daniels, N.3
  • 6
  • 7
    • 41349117788 scopus 로고    scopus 로고
    • Finding community structure in very large networks
    • Clauset, A., Newman, M.E.J., and Moore, C. 2004. Finding community structure in very large networks. Phys. Rev. E 70, 066111.
    • (2004) Phys. Rev. E , vol.70 , pp. 066111
    • Clauset, A.1    Newman, M.E.J.2    Moore, C.3
  • 8
    • 34147121646 scopus 로고    scopus 로고
    • Toward a comprehensive atlas of the physical interactome of saccharomyces cerevisiae
    • Collins, S., Kemmeren, P., Zhao, X., et al. 2007a. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 439
    • Collins, S.1    Kemmeren, P.2    Zhao, X.3
  • 10
    • 0035830860 scopus 로고    scopus 로고
    • Principles for the buffering of genetic variation
    • Hartman, J.L., Garvik, B., and Hartwell, L. 2001. Principles for the buffering of genetic variation. Science 291, 1001-1004.
    • (2001) Science , vol.291 , pp. 1001-1004
    • Hartman, J.L.1    Garvik, B.2    Hartwell, L.3
  • 11
    • 78650263469 scopus 로고    scopus 로고
    • Evaluating between-pathway models with expression data
    • Hescott, B.J., Leiserson, M.D., Cowen, L.J., et al. 2009. Evaluating between-pathway models with expression data. Proc RECOMB 2009 372-385.
    • (2009) Proc RECOMB , vol.2009 , pp. 372-385
    • Hescott, B.J.1    Leiserson, M.D.2    Cowen, L.J.3
  • 12
    • 35748950713 scopus 로고    scopus 로고
    • Exploring the functional landscape of gene expression: Directed search of large microarray compendia
    • DOI 10.1093/bioinformatics/btm403
    • Hibbs, M.A., Hess, D.C., Myers, C.L., et al. 2007. Exploring the functional landscape of gene expression: Directed search of large microarray compendia. Bioinformatics 23, 2692-2699. (Pubitemid 350048333)
    • (2007) Bioinformatics , vol.23 , Issue.20 , pp. 2692-2699
    • Hibbs, M.A.1    Hess, D.C.2    Myers, C.L.3    Huttenhower, C.4    Li, K.5    Troyanskaya, O.G.6
  • 13
    • 33947617347 scopus 로고    scopus 로고
    • Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss
    • Ihmels, J., Collins, S.R., Schuldiner, M., et al. 2007. Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss. Mol. Syst. Biol. 3, 86.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 86
    • Ihmels, J.1    Collins, S.R.2    Schuldiner, M.3
  • 14
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • DOI 10.1038/nbt1096
    • Kelley, R., and Ideker, T. 2005. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561-566. (Pubitemid 41724894)
    • (2005) Nature Biotechnology , vol.23 , Issue.5 , pp. 561-566
    • Kelley, R.1    Ideker, T.2
  • 15
    • 38449099349 scopus 로고    scopus 로고
    • Assessing and combining reliability of protein interaction sources
    • Leach, S., Gabow, A., Hunter, L., et al. 2007. Assessing and combining reliability of protein interaction sources. Pac. Symp. Biocomput. 433-444.
    • (2007) Pac. Symp. Biocomput. , pp. 433-444
    • Leach, S.1    Gabow, A.2    Hunter, L.3
  • 16
    • 44849087833 scopus 로고    scopus 로고
    • Mapping genetically compensatory pathways from synthetic lethal interactions in yeast
    • Ma, X., Tarone, A.M., and Li, W. 2008. Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS ONE 3, e1922.
    • (2008) PLoS ONE , vol.3
    • Ma, X.1    Tarone, A.M.2    Li, W.3
  • 18
    • 59649120244 scopus 로고    scopus 로고
    • Revealing biological modules via graph summarization
    • Navlakha, S., Schatz, M.C., and Kingsford, C. 2009. Revealing biological modules via graph summarization. J. Comput. Biol. 16, 253-264.
    • (2009) J. Comput. Biol. , vol.16 , pp. 253-264
    • Navlakha, S.1    Schatz, M.C.2    Kingsford, C.3
  • 21
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • Stark, C., Breitkreutz, B., Reguly, T., et al. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Res. 34, D535.
    • (2006) Nucleic Acids Res. , vol.34
    • Stark, C.1    Breitkreutz, B.2    Reguly, T.3
  • 24
    • 34247193051 scopus 로고    scopus 로고
    • Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
    • Ulitsky, I., and Shamir, R. 2007. Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol. Syst. Biol. 3, 104.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 104
    • Ulitsky, I.1    Shamir, R.2
  • 25
    • 47349120555 scopus 로고    scopus 로고
    • From E-MAPs to module maps: Dissecting quantitative genetic interactions using physical interactions
    • Ulitsky, I., Shlomi, T., Kupiec, M., et al. 2008. From E-MAPs to module maps: Dissecting quantitative genetic interactions using physical interactions. Mol. Syst. Biol. 4, 209.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 209
    • Ulitsky, I.1    Shlomi, T.2    Kupiec, M.3
  • 26
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • DOI 10.1038/nbt825
    • Vazquez, A., Flammini, A., Maritan, A., et al. 2003. Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 21, 697-700. (Pubitemid 36638099)
    • (2003) Nature Biotechnology , vol.21 , Issue.6 , pp. 697-700
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.