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Volumn 20, Issue 8, 2010, Pages 1143-1153

Predicting genetic modifier loci using functional gene networks

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE INTERACTION; GENE LOCUS; GENE MUTATION; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SACCHAROMYCES CEREVISIAE;

EID: 77954760095     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.102749.109     Document Type: Article
Times cited : (69)

References (75)
  • 1
    • 65349085291 scopus 로고    scopus 로고
    • Global networks of functional coupling in eukaryotes from comprehensive data integration
    • Alexeyenko A, Sonnhammer EL. 2009. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res 19: 1107-1116.
    • (2009) Genome Res , vol.19 , pp. 1107-1116
    • Alexeyenko, A.1    Sonnhammer, E.L.2
  • 4
    • 45449095236 scopus 로고    scopus 로고
    • Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men
    • doi: 10.1371/journal.pone.0001593
    • Bochdanovits Z, Sondervan D, Perillous S, van Beijsterveldt T, Boomsma D, Heutink P. 2008. Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men. PLoS One 3: e1593. doi: 10.1371/journal.pone.0001593.
    • (2008) PLoS One , vol.3
    • Bochdanovits, Z.1    Sondervan, D.2    Perillous, S.3    Van Beijsterveldt, T.4    Boomsma, D.5    Heutink, P.6
  • 5
    • 43949108579 scopus 로고    scopus 로고
    • Getting up close and personal with your genome
    • Bonetta L. 2008. Getting up close and personal with your genome. Cell 133: 753-756.
    • (2008) Cell , vol.133 , pp. 753-756
    • Bonetta, L.1
  • 6
    • 34249041230 scopus 로고    scopus 로고
    • Exploring genetic interactions and networks with yeast
    • DOI 10.1038/nrg2085, PII NRG2085
    • Boone C, Bussey H, Andrews BJ. 2007. Exploring genetic interactions and networks with yeast. Nat Rev Genet 8: 437-449. (Pubitemid 46789246)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.6 , pp. 437-449
    • Boone, C.1    Bussey, H.2    Andrews, B.J.3
  • 13
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • DOI 10.1016/S0968-0004(98)01274-2, PII S0968000498012742
    • Dandekar T, Snel B, Huynen M, Bork P. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324-328. (Pubitemid 28461862)
    • (1998) Trends in Biochemical Sciences , vol.23 , Issue.9 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 14
    • 0041358614 scopus 로고    scopus 로고
    • Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
    • Date SV, Marcotte EM. 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 21: 1055-1062.
    • (2003) Nat Biotechnol , vol.21 , pp. 1055-1062
    • Date, S.V.1    Marcotte, E.M.2
  • 18
    • 66049159816 scopus 로고    scopus 로고
    • Genetic architecture of quantitative traits in mice, flies, and humans
    • Flint J, Mackay TF. 2009. Genetic architecture of quantitative traits in mice, flies, and humans. Genome Res 19: 723-733.
    • (2009) Genome Res , vol.19 , pp. 723-733
    • Flint, J.1    Mackay, T.F.2
  • 19
    • 2642566695 scopus 로고    scopus 로고
    • A probabilistic view of gene function
    • Fraser AG, Marcotte EM. 2004. A probabilistic view of gene function. Nat Genet 36: 559-564.
    • (2004) Nat Genet , vol.36 , pp. 559-564
    • Fraser, A.G.1    Marcotte, E.M.2
  • 20
    • 43249125341 scopus 로고    scopus 로고
    • Using protein complexes to predict phenotypic effects of gene mutation
    • doi: 10.1186/gb-2007-8-11-r252
    • Fraser HB, Plotkin JB. 2007. Using protein complexes to predict phenotypic effects of gene mutation. Genome Biol 8: R252. doi: 10.1186/gb-2007-8-11-r252.
    • (2007) Genome Biol , vol.8
    • Fraser, H.B.1    Plotkin, J.B.2
  • 21
    • 0032489430 scopus 로고    scopus 로고
    • The VAB-1 Eph receptor tyrosine kinase functions in neural and epithelial morphogenesis in C. elegans
    • DOI 10.1016/S0092-8674(00)81131-9
    • George SE, Simokat K, Hardin J, Chisholm AD. 1998. The VAB-1 Eph receptor tyrosine kinase functions in neural and epithelial morphogenesis in C. elegans. Cell 92: 633-643. (Pubitemid 28141512)
    • (1998) Cell , vol.92 , Issue.5 , pp. 633-643
    • George, S.E.1    Simokat, K.2    Hardin, J.3    Chisholm, A.D.4
  • 24
    • 34547787599 scopus 로고    scopus 로고
    • A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
    • DOI 10.1186/1471-2105-8-236
    • Hart GT, Lee I, Marcotte EM. 2007. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 8: 236. doi: 10.1186/1471-2105-8-236. (Pubitemid 47225392)
    • (2007) BMC Bioinformatics , vol.8 , pp. 236
    • Hart, G.T.1    Lee, I.2    Marcotte, E.R.3
  • 25
    • 0035830860 scopus 로고    scopus 로고
    • Principles for the buffering of genetic variation
    • Hartman J, Garvik B, Hartwell L. 2001. Principles for the buffering of genetic variation. Science 291: 1001-1004.
    • (2001) Science , vol.291 , pp. 1001-1004
    • Hartman, J.1    Garvik, B.2    Hartwell, L.3
  • 26
    • 0033634782 scopus 로고    scopus 로고
    • ARK-1 inhibits EGFR signaling in C. elegans
    • Hopper NA, Lee J, Sternberg PW. 2000. ARK-1 inhibits EGFR signaling in C. elegans. Mol Cell 6: 65-75.
    • (2000) Mol Cell , vol.6 , pp. 65-75
    • Hopper, N.A.1    Lee, J.2    Sternberg, P.W.3
  • 28
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
    • Huynen M, Snel B, Lathe W III, Bork P. 2000. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res 10: 1204-1210.
    • (2000) Genome Res , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe III, W.3    Bork, P.4
  • 32
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • DOI 10.1038/nbt1096
    • Kelley R, 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
  • 35
    • 47549098627 scopus 로고    scopus 로고
    • Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
    • doi: 10.1186/gb-2008-9-s1-s5
    • Kim WK, Krumpelman C, Marcotte EM. 2008. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol 9: S5. doi: 10.1186/gb-2008-9-s1-s5.
    • (2008) Genome Biol , vol.9
    • Kim, W.K.1    Krumpelman, C.2    Marcotte, E.M.3
  • 37
    • 53849103270 scopus 로고    scopus 로고
    • Modeling synthetic lethality
    • doi: 10.1186/gb-2009-9-9-r135
    • Le Meur N, Gentleman R. 2008. Modeling synthetic lethality. Genome Biol 9: R135. doi: 10.1186/gb-2009-9-9-r135.
    • (2008) Genome Biol , vol.9
    • Le Meur, N.1    Gentleman, R.2
  • 38
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • DOI 10.1126/science.1099511
    • Lee I, Date SV, Adai AT, Marcotte EM. 2004. A probabilistic functional network of yeast genes. Science 306: 1555-1558. (Pubitemid 39564951)
    • (2004) Science , vol.306 , Issue.5701 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 39
    • 41549138299 scopus 로고    scopus 로고
    • An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae
    • doi: 10.1371/journal.pone.0000988
    • Lee I, Li Z, Marcotte EM. 2007. An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One 2: e988. doi: 10.1371/journal.pone.0000988.
    • (2007) PLoS One , vol.2
    • Lee, I.1    Li, Z.2    Marcotte, E.M.3
  • 40
    • 38649138295 scopus 로고    scopus 로고
    • A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
    • DOI 10.1038/ng.2007.70, PII NG200770
    • Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM. 2008. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40: 181-188. (Pubitemid 351171397)
    • (2008) Nature Genetics , vol.40 , Issue.2 , pp. 181-188
    • Lee, I.1    Lehner, B.2    Crombie, C.3    Wong, W.4    Fraser, A.G.5    Marcotte, E.M.6
  • 41
    • 34249732505 scopus 로고    scopus 로고
    • Modelling genotype-phenotype relationships and human disease with genetic interaction networks
    • DOI 10.1242/jeb.002311
    • Lehner B. 2007. Modelling genotype-phenotype relationships and human disease with genetic interaction networks. J Exp Biol 210: 1559-1566. (Pubitemid 46841960)
    • (2007) Journal of Experimental Biology , vol.210 , Issue.9 , pp. 1559-1566
    • Lehner, B.1
  • 42
    • 33746525415 scopus 로고    scopus 로고
    • Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways
    • DOI 10.1038/ng1844, PII NG1844
    • Lehner B, Crombie C, Tischler J, Fortunato A, Fraser AG. 2006a. Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways. Nat Genet 38: 896-903. (Pubitemid 44141657)
    • (2006) Nature Genetics , vol.38 , Issue.8 , pp. 896-903
    • Lehner, B.1    Crombie, C.2    Tischler, J.3    Fortunato, A.4    Fraser, A.G.5
  • 43
    • 34249740079 scopus 로고    scopus 로고
    • RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions
    • Lehner B, Tischler J, Fraser AG. 2006b. RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat Protoc 1: 1617-1620.
    • (2006) Nat Protoc , vol.1 , pp. 1617-1620
    • Lehner, B.1    Tischler, J.2    Fraser, A.G.3
  • 45
    • 48749114997 scopus 로고    scopus 로고
    • A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation
    • Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD. 2008. A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev 22: 2062-2074.
    • (2008) Genes Dev , vol.22 , pp. 2062-2074
    • Lin, Y.Y.1    Qi, Y.2    Lu, J.Y.3    Pan, X.4    Yuan, D.S.5    Zhao, Y.6    Bader, J.S.7    Boeke, J.D.8
  • 46
    • 76249105279 scopus 로고    scopus 로고
    • Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
    • doi: 10.1186/gb-2009-10-9-r91
    • Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C. 2009. Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol 10: R91. doi: 10.1186/gb-2009-10-9-r91.
    • (2009) Genome Biol , vol.10
    • Linghu, B.1    Snitkin, E.S.2    Hu, Z.3    Xia, Y.4    Delisi, C.5
  • 47
    • 67651108806 scopus 로고    scopus 로고
    • The genetics of quantitative traits: Challenges and prospects
    • Mackay TF, Stone EA, Ayroles JF. 2009. The genetics of quantitative traits: Challenges and prospects. Nat Rev Genet 10: 565-577.
    • (2009) Nat Rev Genet , vol.10 , pp. 565-577
    • Mackay, T.F.1    Stone, E.A.2    Ayroles, J.F.3
  • 48
    • 55549147191 scopus 로고    scopus 로고
    • Personal genomes: The case of the missing heritability
    • Maher B. 2008. Personal genomes: The case of the missing heritability. Nature 456: 18-21.
    • (2008) Nature , vol.456 , pp. 18-21
    • Maher, B.1
  • 49
    • 0033523854 scopus 로고    scopus 로고
    • A combined algorithm for genome-wide prediction of protein function
    • DOI 10.1038/47048
    • Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. 1999. A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86. (Pubitemid 29533519)
    • (1999) Nature , vol.402 , Issue.6757 , pp. 83-86
    • Marcotte, E.M.1    Pellegrini, M.2    Thompson, M.J.3    Yeates, T.O.4    Eisenberg, D.5
  • 50
    • 40449107017 scopus 로고    scopus 로고
    • Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes
    • DOI 10.1186/gb-2007-8-12-r258
    • McGary KL, Lee I, Marcotte EM. 2007. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol 8: R258. doi: 10.1186/gb-2007-8-12-r258. (Pubitemid 351934064)
    • (2007) Genome Biology , vol.8 , Issue.12
    • McGary, K.L.1    Lee, I.2    Marcotte, E.M.3
  • 52
    • 34548749776 scopus 로고    scopus 로고
    • Context-sensitive data integration and prediction of biological networks
    • DOI 10.1093/bioinformatics/btm332
    • Myers CL, Troyanskaya OG. 2007. Context-sensitive data integration and prediction of biological networks. Bioinformatics 23: 2322-2330. (Pubitemid 47423871)
    • (2007) Bioinformatics , vol.23 , Issue.17 , pp. 2322-2330
    • Myers, C.L.1    Troyanskaya, O.G.2
  • 54
    • 33644778778 scopus 로고    scopus 로고
    • A DNA integrity network in the yeast Saccharomyces cerevisiae
    • DOI 10.1016/j.cell.2005.12.036, PII S0092867406001188
    • Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. 2006. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124: 1069-1081. (Pubitemid 43344244)
    • (2006) Cell , vol.124 , Issue.5 , pp. 1069-1081
    • Pan, X.1    Ye, P.2    Yuan, D.S.3    Wang, X.4    Bader, J.S.5    Boeke, J.D.6
  • 57
    • 57149103917 scopus 로고    scopus 로고
    • Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions
    • Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. 2008. Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 18: 1991-2004.
    • (2008) Genome Res , vol.18 , pp. 1991-2004
    • Qi, Y.1    Suhail, Y.2    Lin, Y.Y.3    Boeke, J.D.4    Bader, J.S.5
  • 58
    • 42149116826 scopus 로고    scopus 로고
    • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    • doi: 10.1038/msb.2008.19
    • Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM. 2008. A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol 4: 180. doi: 10.1038/msb.2008.19.
    • (2008) Mol Syst Biol , vol.4 , pp. 180
    • Ramani, A.K.1    Li, Z.2    Hart, G.T.3    Carlson, M.W.4    Boutz, D.R.5    Marcotte, E.M.6
  • 59
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • DOI 10.1006/jmbi.2000.5197
    • Remm M, Storm CE, Sonnhammer EL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052. (Pubitemid 34073068)
    • (2001) Journal of Molecular Biology , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.V.2    Sonnhammer, E.L.L.3
  • 61
    • 0036259723 scopus 로고    scopus 로고
    • A lin-45 raf enhancer screen identifies eor-1, eor-2 and unusual alleles of Ras pathway genes in Caenorhabditis elegans
    • Rocheleau CE, Howard RM, Goldman AP, Volk ML, Girard LJ, Sundaram MV. 2002. A lin-45 raf enhancer screen identifies eor-1, eor-2 and unusual alleles of Ras pathway genes in Caenorhabditis elegans. Genetics 161: 121-131.
    • (2002) Genetics , vol.161 , pp. 121-131
    • Rocheleau, C.E.1    Howard, R.M.2    Goldman, A.P.3    Volk, M.L.4    Girard, L.J.5    Sundaram, M.V.6
  • 66
  • 67
    • 41349102391 scopus 로고    scopus 로고
    • Evolutionary plasticity of genetic interaction networks
    • DOI 10.1038/ng.114, PII NG114
    • Tischler J, Lehner B, Fraser AG. 2008. Evolutionary plasticity of genetic interaction networks. Nat Genet 40: 390-391. (Pubitemid 351450883)
    • (2008) Nature Genetics , vol.40 , Issue.4 , pp. 390-391
    • Tischler, J.1    Lehner, B.2    Fraser, A.G.3
  • 70
    • 34247193051 scopus 로고    scopus 로고
    • Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
    • DOI 10.1038/msb4100144, PII MSB4100144
    • Ulitsky I, Shamir R. 2007. Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol 3: 104. (Pubitemid 46625178)
    • (2007) Molecular Systems Biology , vol.3 , pp. 104
    • Ulitsky, I.1    Shamir, R.2
  • 72
    • 0035085816 scopus 로고    scopus 로고
    • Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
    • Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV. 2001. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 11: 356-372.
    • (2001) Genome Res , vol.11 , pp. 356-372
    • Wolf, Y.I.1    Rogozin, I.B.2    Kondrashov, A.S.3    Koonin, E.V.4
  • 74
    • 33746898247 scopus 로고    scopus 로고
    • Gene function prediction from congruent synthetic lethal interactions in yeast
    • 2005.0026. doi: 10.1038/msb4200034
    • Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS. 2005. Gene function prediction from congruent synthetic lethal interactions in yeast. Mol Syst Biol 1: 2005.0026. doi: 10.1038/msb4200034.
    • (2005) Mol Syst Biol , vol.1
    • Ye, P.1    Peyser, B.D.2    Pan, X.3    Boeke, J.D.4    Spencer, F.A.5    Bader, J.S.6
  • 75
    • 33644864549 scopus 로고    scopus 로고
    • Genome-wide prediction of C. elegans genetic interactions
    • DOI 10.1126/science.1123287
    • Zhong W, Sternberg PW. 2006. Genome-wide prediction of C. elegans genetic interactions. Science 311: 1481-1484. (Pubitemid 43376706)
    • (2006) Science , vol.311 , Issue.5766 , pp. 1481-1484
    • Zhong, W.1    Sternberg, P.W.2


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