메뉴 건너뛰기




Volumn 198, Issue 4, 2014, Pages 1377-1393

Mapping eQTL networks with mixed graphical Markov models

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 3; EXPRESSION QUANTITATIVE TRAIT LOCUS NETWORK MAPPING; FUNGAL GENE; FUNGAL STRAIN; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE REGULATORY NETWORK; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; HEREDITY; HIGHE RORDER CONDITIONAL INDEPENDENCE; INTERMETHOD COMPARISON; MIXED GRAPHICAL MARKOV MODEL; NONHUMAN; Q ORDER CORRELATION GRAPH; QUANTITATIVE TRAIT LOCUS MAPPING; STATISTICAL MODEL; STATISTICAL PARAMETERS; YEAST; ALGORITHM; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER PROGRAM; CROSS BREEDING; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; PROBABILITY; PROCEDURES; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY;

EID: 84915747992     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.169573     Document Type: Article
Times cited : (11)

References (60)
  • 2
    • 22144454660 scopus 로고    scopus 로고
    • Genetical genomics analysis of a yeast segregant population for transcription network inference
    • Bing, N., and I. Hoeschele, 2005 Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics 170: 533-542.
    • (2005) Genetics , vol.170 , pp. 533-542
    • Bing, N.1    Hoeschele, I.2
  • 3
    • 84873722165 scopus 로고    scopus 로고
    • Finding the sources of missing heritability in a yeast cross
    • Bloom, J. S., I. M. Ehrenreich, W. T. Loo, T.-L. V. Lite, and L. Kruglyak, 2013 Finding the sources of missing heritability in a yeast cross. Nature 494: 234-237.
    • (2013) Nature , vol.494 , pp. 234-237
    • Bloom, J.S.1    Ehrenreich, I.M.2    Loo, W.T.3    Lite, T.-L.V.4    Kruglyak, L.5
  • 4
  • 5
    • 13444306165 scopus 로고    scopus 로고
    • The landscape of genetic complexity across 5,700 gene expression traits in yeast
    • Brem, R. B., and L. Kruglyak, 2005 The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA 102: 1572-1577.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1572-1577
    • Brem, R.B.1    Kruglyak, L.2
  • 6
    • 0037177625 scopus 로고    scopus 로고
    • Genetic dissection of transcriptional regulation in budding yeast
    • Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak, 2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
    • (2002) Science , vol.296 , pp. 752-755
    • Brem, R.B.1    Yvert, G.2    Clinton, R.3    Kruglyak, L.4
  • 9
    • 33845523872 scopus 로고    scopus 로고
    • A robust procedure for Gaussian graphical model search from microarray data with p larger than n
    • Castelo, R., and A. Roverato, 2006 A robust procedure for Gaussian graphical model search from microarray data with p larger than n. J. Mach. Learn. Res. 7: 2621-2650.
    • (2006) J. Mach. Learn. Res , vol.7 , pp. 2621-2650
    • Castelo, R.1    Roverato, A.2
  • 10
    • 59649121280 scopus 로고    scopus 로고
    • Reverse engineering molecular regulatory networks from microarray data with qp-graphs
    • Castelo, R., and A. Roverato, 2009 Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comput. Biol. 16: 213-227.
    • (2009) J. Comput. Biol , vol.16 , pp. 213-227
    • Castelo, R.1    Roverato, A.2
  • 11
    • 49849090353 scopus 로고    scopus 로고
    • Inferring causal phenotype networks from segregating populations
    • Chaibub Neto, E., C. T. Ferrara, A. D. Attie, and B. S. Yandell, 2008 Inferring causal phenotype networks from segregating populations. Genetics 179: 1089-1100.
    • (2008) Genetics , vol.179 , pp. 1089-1100
    • Chaibub Neto, E.1    Ferrara, C.T.2    Attie, A.D.3    Yandell, B.S.4
  • 12
    • 84870284276 scopus 로고    scopus 로고
    • Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes
    • Chaibub Neto, E., M. P. Keller, A. D. Attie, and B. S. Yandell, 2010 Causal graphical models in systems genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann. Appl. Stat. 4: 320-339.
    • (2010) Ann. Appl. Stat , vol.4 , pp. 320-339
    • Chaibub Neto, E.1    Keller, M.P.2    Attie, A.D.3    Yandell, B.S.4
  • 13
    • 84876452797 scopus 로고    scopus 로고
    • Modeling causality for pairs of phenotypes in systems genetics
    • Chaibub Neto, E., A. T. Broman, M. P. Keller, A. D. Attie, B. Zhang et al., 2013 Modeling causality for pairs of phenotypes in systems genetics. Genetics 193: 1003-1013.
    • (2013) Genetics , vol.193 , pp. 1003-1013
    • Chaibub Neto, E.1    Broman, A.T.2    Keller, M.P.3    Attie, A.D.4    Zhang, B.5
  • 14
    • 42949144555 scopus 로고    scopus 로고
    • Harnessing naturally randomized transcription to infer regulatory relationships among genes
    • Chen, L. S., F. Emmert-Streib, and J. D. Storey, 2007 Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol. 8: R219.
    • (2007) Genome Biol , vol.8 , pp. R219
    • Chen, L.S.1    Emmert-Streib, F.2    Storey, J.D.3
  • 15
    • 68949211709 scopus 로고    scopus 로고
    • Genetics of human gene expression: Mapping DNA variants that influence gene expression
    • Cheung, V. G., and R. S. Spielman, 2009 Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat. Rev. Genet. 10: 595-604.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 595-604
    • Cheung, V.G.1    Spielman, R.S.2
  • 16
    • 45849120994 scopus 로고    scopus 로고
    • Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways
    • Chin, C.-S., V. Chubukov, E. R. Jolly, J. DeRisi, and H. Li, 2008 Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol. 6: e146.
    • (2008) PLoS Biol , vol.6
    • Chin, C.-S.1    Chubukov, V.2    Jolly, E.R.3    De Risi, J.4    Li, H.5
  • 17
    • 67849118749 scopus 로고    scopus 로고
    • Expression quantitative trait loci mapping with multivariate sparse partial least squares regression
    • Chun, H., and S. Keleş, 2009 Expression quantitative trait loci mapping with multivariate sparse partial least squares regression. Genetics 182: 79-90.
    • (2009) Genetics , vol.182 , pp. 79-90
    • Chun, H.1    Keleş, S.2
  • 19
    • 84875203794 scopus 로고    scopus 로고
    • Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules
    • Curtis, R. E., S. Kim, J. L. Woolford, Jr., W. Xu, and E. P. Xing, 2013 Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules. BMC Genomics 14: 1-17.
    • (2013) BMC Genomics , vol.14 , pp. 1-17
    • Curtis, R.E.1    Kim, S.2    Woolford, J.L.3    Xu, W.4    Xing, E.P.5
  • 20
    • 10444281626 scopus 로고    scopus 로고
    • Collapsibility of graphical cgregression models
    • Didelez, V., and D. Edwards, 2004 Collapsibility of graphical cgregression models. Scand. J. Stat. 31: 535-551.
    • (2004) Scand. J. Stat , vol.31 , pp. 535-551
    • Didelez, V.1    Edwards, D.2
  • 22
    • 76949106424 scopus 로고    scopus 로고
    • Selecting high-dimensional mixed graphical models using minimal aic or bic forests
    • Edwards, D., G. C. G. de Abreu, and R. Labouriau, 2010 Selecting high-dimensional mixed graphical models using minimal aic or bic forests. BMC Bioinformatics 11: 18.
    • (2010) BMC Bioinformatics , vol.11 , pp. 18
    • Edwards, D.1    de Abreu, G.C.G.2    Labouriau, R.3
  • 23
    • 47849109874 scopus 로고
    • Positive definite completions of partial Hermitian matrices
    • Grone, R., C. Johnson, E. Sá, and H. Wolkowicz, 1984 Positive definite completions of partial Hermitian matrices. Linear Algebra Appl. 58: 109-124.
    • (1984) Linear Algebra Appl , vol.58 , pp. 109-124
    • Grone, R.1    Johnson, C.2    Sá, E.3    Wolkowicz, H.4
  • 26
    • 0034616930 scopus 로고    scopus 로고
    • Functional discovery via a compendium of expression profiles
    • Hughes, T. R., M. J. Marton, A. R. Jones, C. J. Roberts, R. Stoughton et al., 2000 Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
    • (2000) Cell , vol.102 , pp. 109-126
    • Hughes, T.R.1    Marton, M.J.2    Jones, A.R.3    Roberts, C.J.4    Stoughton, R.5
  • 27
    • 0035400051 scopus 로고    scopus 로고
    • Genetical genomics: The added value from segregation
    • Jansen, R. C., and J.-P. Nap, 2001 Genetical genomics: the added value from segregation. Trends Genet. 17: 388-390.
    • (2001) Trends Genet , vol.17 , pp. 388-390
    • Jansen, R.C.1    Nap, J.-P.2
  • 28
    • 33947524259 scopus 로고    scopus 로고
    • Estimating high-dimensional directed acyclic graphs with the pc-algorithm
    • Kalisch, M., and P. Bühlmann, 2007 Estimating high-dimensional directed acyclic graphs with the pc-algorithm. J. Mach. Learn. Res. 8: 613-636.
    • (2007) J. Mach. Learn. Res , vol.8 , pp. 613-636
    • Kalisch, M.1    Bühlmann, P.2
  • 29
    • 77950825718 scopus 로고    scopus 로고
    • Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples
    • Kang, E. Y., C. Ye, I. Shpitser, and E. Eskin, 2010 Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples. J. Comput. Biol. 17: 533-546.
    • (2010) J. Comput. Biol , vol.17 , pp. 533-546
    • Kang, E.Y.1    Ye, C.2    Shpitser, I.3    Eskin, E.4
  • 30
    • 61849171085 scopus 로고    scopus 로고
    • Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots
    • Kang, H. M., C. Ye, and E. Eskin, 2008 Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics 180: 1909-1925.
    • (2008) Genetics , vol.180 , pp. 1909-1925
    • Kang, H.M.1    Ye, C.2    Eskin, E.3
  • 31
    • 33645068841 scopus 로고    scopus 로고
    • Statistical methods for expression quantitative trait loci (eQTL) mapping
    • Kendziorski, C., M. Chen, M. Yuan, H. Lan, and A. Attie, 2006 Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62: 19-27.
    • (2006) Biometrics , vol.62 , pp. 19-27
    • Kendziorski, C.1    Chen, M.2    Yuan, M.3    Lan, H.4    Attie, A.5
  • 32
    • 70149098541 scopus 로고    scopus 로고
    • Statistical estimation of correlated genome associations to a quantitative trait network
    • Kim, S., and E. P. Xing, 2009 Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet. 5: e1000587.
    • (2009) PLoS Genet , vol.5
    • Kim, S.1    Xing, E.P.2
  • 33
    • 84860916660 scopus 로고    scopus 로고
    • Hive plots: Rational approach to visualizing networks
    • Krzywinski, M., I. Birol, S. J. Jones, and M. A. Marra, 2012 Hive plots: rational approach to visualizing networks. Brief. Bioinform. 13: 627-644.
    • (2012) Brief. Bioinform , vol.13 , pp. 627-644
    • Krzywinski, M.1    Birol, I.2    Jones, S.J.3    Marra, M.A.4
  • 34
    • 0004047518 scopus 로고    scopus 로고
    • Oxford University Press, Oxford
    • Lauritzen, S., 1996 Graphical Models. Oxford University Press, Oxford.
    • (1996) Graphical Models
    • Lauritzen, S.1
  • 35
    • 0002480085 scopus 로고
    • Graphical models for associations between variables, some of which are qualitative and some quantitative
    • Lauritzen, S., and N. Wermuth, 1989 Graphical models for associations between variables, some of which are qualitative and some quantitative. Ann. Stat. 17: 31-57.
    • (1989) Ann. Stat , vol.17 , pp. 31-57
    • Lauritzen, S.1    Wermuth, N.2
  • 36
    • 79952489475 scopus 로고    scopus 로고
    • Estimating missing heritability for disease from genomewide association studies
    • Lee, S. H., N. R. Wray, M. E. Goddard, and P. M. Visscher, 2011 Estimating missing heritability for disease from genomewide association studies. Am. J. Hum. Genet. 88: 294-305.
    • (2011) Am. J. Hum. Genet , vol.88 , pp. 294-305
    • Lee, S.H.1    Wray, N.R.2    Goddard, M.E.3    Visscher, P.M.4
  • 37
    • 34848914038 scopus 로고    scopus 로고
    • Capturing heterogeneity in gene expression studies by surrogate variable analysis
    • Leek, J. T., and J. D. Storey, 2007 Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3: e161.
    • (2007) PLoS Genet , vol.3
    • Leek, J.T.1    Storey, J.D.2
  • 38
    • 77956873627 scopus 로고    scopus 로고
    • Tackling the widespread and critical impact of batch effects in high-throughput data
    • Leek, J. T., R. B. Scharpf, H. C. Bravo, D. Simcha, B. Langmead et al., 2010 Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 11: 733-739.
    • (2010) Nat. Rev. Genet , vol.11 , pp. 733-739
    • Leek, J.T.1    Scharpf, R.B.2    Bravo, H.C.3    Simcha, D.4    Langmead, B.5
  • 40
    • 78049312702 scopus 로고    scopus 로고
    • Correction for hidden confounders in the genetic analysis of gene expression
    • Listgarten, J., C. Kadie, and D. Heckerman, 2010 Correction for hidden confounders in the genetic analysis of gene expression. Proc. Natl. Acad. Sci. USA 107: 16465-16470.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 16465-16470
    • Listgarten, J.1    Kadie, C.2    Heckerman, D.3
  • 41
    • 45149096374 scopus 로고    scopus 로고
    • Gene network inference via structural equation modeling in genetical genomics experiments
    • Liu, B., A. de la Fuente, and I. Hoeschele, 2008 Gene network inference via structural equation modeling in genetical genomics experiments. Genetics 178: 1763-1776.
    • (2008) Genetics , vol.178 , pp. 1763-1776
    • Liu, B.1    de la Fuente, A.2    Hoeschele, I.3
  • 43
    • 77950458649 scopus 로고    scopus 로고
    • Transcriptome genetics using second generation sequencing in a Caucasian population
    • Montgomery, S. B., M. Sammeth, M. Gutierrez-Arcelus, R. P. Lach, C. Ingle et al., 2010 Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773- 777.
    • (2010) Nature , vol.464 , pp. 773-777
    • Montgomery, S.B.1    Sammeth, M.2    Gutierrez-Arcelus, M.3    Lach, R.P.4    Ingle, C.5
  • 44
    • 79851507206 scopus 로고    scopus 로고
    • Joint genetic analysis of gene expression data with inferred cellular phenotypes
    • Parts, L., O. Stegle, J. Winn, and R. Durbin, 2011 Joint genetic analysis of gene expression data with inferred cellular phenotypes. PLoS Genet. 7: e1001276.
    • (2011) PLoS Genet , vol.7
    • Parts, L.1    Stegle, O.2    Winn, J.3    Durbin, R.4
  • 45
    • 33750481513 scopus 로고    scopus 로고
    • Heritability and tissue specificity of expression quantitative trait loci
    • Petretto, E., J. Mangion, N. J. Dickens, S. A. Cook, M. K. Kumaran et al., 2006 Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet. 2: e172.
    • (2006) PLoS Genet , vol.2
    • Petretto, E.1    Mangion, J.2    Dickens, N.J.3    Cook, S.A.4    Kumaran, M.K.5
  • 47
    • 35748949257 scopus 로고    scopus 로고
    • A comparison of background correction methods for two-colour microarrays
    • Ritchie, M. E., J. Silver, A. Oshlack, M. Holmes, D. Diyagama et al., 2007 A comparison of background correction methods for two-colour microarrays. Bioinformatics 23: 2700-2707.
    • (2007) Bioinformatics , vol.23 , pp. 2700-2707
    • Ritchie, M.E.1    Silver, J.2    Oshlack, A.3    Holmes, M.4    Diyagama, D.5
  • 48
    • 57649124192 scopus 로고    scopus 로고
    • Reverse engineering the genotype- phenotype map with natural genetic variation
    • Rockman, M. V., 2008 Reverse engineering the genotype- phenotype map with natural genetic variation. Nature 456: 738-744.
    • (2008) Nature , vol.456 , pp. 738-744
    • Rockman, M.V.1
  • 49
    • 33750204290 scopus 로고    scopus 로고
    • Genetics of global gene expression
    • Rockman, M. V., and L. Kruglyak, 2006 Genetics of global gene expression. Nat. Rev. Genet. 7: 862-872.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 862-872
    • Rockman, M.V.1    Kruglyak, L.2
  • 50
    • 0035995077 scopus 로고    scopus 로고
    • Hyper inverse Wishart distribution for nondecomposable graphs and its application to Bayesian inference for Gaussian graphical models
    • Roverato, A., 2002 Hyper inverse Wishart distribution for nondecomposable graphs and its application to Bayesian inference for Gaussian graphical models. Scand. J. Stat. 29: 391-411.
    • (2002) Scand. J. Stat , vol.29 , pp. 391-411
    • Roverato, A.1
  • 51
    • 0037456823 scopus 로고    scopus 로고
    • Genetics of gene expression surveyed in maize, mouse and man
    • Schadt, E. E., S. A. Monks, T. A. Drake, A. J. Lusis, N. Che et al., 2003 Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
    • (2003) Nature , vol.422 , pp. 297-302
    • Schadt, E.E.1    Monks, S.A.2    Drake, T.A.3    Lusis, A.J.4    Che, N.5
  • 53
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth, G. K., and T. Speed, 2003 Normalization of cDNA microarray data. Methods 31: 265-273.
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 54
    • 77955505742 scopus 로고    scopus 로고
    • A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies
    • Stegle, O., L. Parts, R. Durbin, and J. Winn, 2010 A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLOS Comput. Biol. 6: e1000770.
    • (2010) PLOS Comput. Biol , vol.6
    • Stegle, O.1    Parts, L.2    Durbin, R.3    Winn, J.4
  • 55
    • 84891806965 scopus 로고    scopus 로고
    • The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
    • Teixeira, M. C., P. T. Monteiro, J. F. Guerreiro, J. P. Gonçalves, N. P. Mira et al., 2014 The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 42: D161-D166.
    • (2014) Nucleic Acids Res , vol.42 , pp. D161-D166
    • Teixeira, M.C.1    Monteiro, P.T.2    Guerreiro, J.F.3    Gonçalves, J.P.4    Mira, N.P.5
  • 57
    • 84885018609 scopus 로고    scopus 로고
    • Systematic identification of trans eQTLs as putative drivers of known disease associations
    • Westra, H.-J., M. J. Peters, T. Esko, H. Yaghootkar, C. Schurmann et al., 2013 Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 45: 1238-1243.
    • (2013) Nat. Genet , vol.45 , pp. 1238-1243
    • Westra, H.-J.1    Peters, M.J.2    Esko, T.3    Yaghootkar, H.4    Schurmann, C.5
  • 58
    • 0042856391 scopus 로고    scopus 로고
    • Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
    • Yvert, G., R. B. Brem, J. Whittle, J. M. Akey, E. Foss et al., 2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35: 57-64.
    • (2003) Nat. Genet , vol.35 , pp. 57-64
    • Yvert, G.1    Brem, R.B.2    Whittle, J.3    Akey, J.M.4    Foss, E.5
  • 59
    • 3242806720 scopus 로고    scopus 로고
    • An integrative genomics approach to the reconstruction of gene networks in segregating populations
    • Zhu, J., P. Y. Lum, J. Lamb, D. GuhaThakurta, S. W. Edwards et al., 2004 An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet. Genome Res. 105: 363-374.
    • (2004) Cytogenet. Genome Res , vol.105 , pp. 363-374
    • Zhu, J.1    Lum, P.Y.2    Lamb, J.3    Guha Thakurta, D.4    Edwards, S.W.5
  • 60
    • 45149106353 scopus 로고    scopus 로고
    • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
    • Zhu, J., B. Zhang, E. N. Smith, B. Drees, R. B. Brem et al., 2008 Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat. Genet. 40: 854-861.
    • (2008) Nat. Genet , vol.40 , pp. 854-861
    • Zhu, J.1    Zhang, B.2    Smith, E.N.3    Drees, B.4    Brem, R.B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.