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Volumn 8, Issue 6, 2013, Pages

An Information-Theoretic Machine Learning Approach to Expression QTL Analysis

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANIMAL EXPERIMENT; ARTICLE; CALCULATION; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; GENE FREQUENCY; GENETIC MARKER; GENOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; INCREMENTAL FEATURE SELECTION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; MACHINE LEARNING; MALE; MAXIMUM RELEVANCE MINIMUM REDUNDANCY; MOUSE; NONHUMAN; QUANTITATIVE TRAIT LOCUS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84879386452     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067899     Document Type: Article
Times cited : (29)

References (53)
  • 1
    • 47249142778 scopus 로고    scopus 로고
    • Revealing the architecture of gene regulation: the promise of eQTL studies
    • Gilad Y, Rifkin SA, Pritchard JK, (2008) Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 24: 408-415.
    • (2008) Trends Genet , vol.24 , pp. 408-415
    • Gilad, Y.1    Rifkin, S.A.2    Pritchard, J.K.3
  • 3
    • 0037177625 scopus 로고    scopus 로고
    • Genetic dissection of transcriptional regulation in budding yeast
    • Brem RB, Yvert G, Clinton R, Kruglyak L, (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
  • 4
    • 0037456823 scopus 로고    scopus 로고
    • Genetics of gene expression surveyed in maize, mouse and man
    • Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, 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
  • 5
    • 65249170333 scopus 로고    scopus 로고
    • Genetic analysis of radiation-induced changes in human gene expression
    • Smirnov DA, Morley M, Shin E, Spielman RS, Cheung VG, (2009) Genetic analysis of radiation-induced changes in human gene expression. Nature 459: 587-591.
    • (2009) Nature , vol.459 , pp. 587-591
    • Smirnov, D.A.1    Morley, M.2    Shin, E.3    Spielman, R.S.4    Cheung, V.G.5
  • 6
    • 67649867440 scopus 로고    scopus 로고
    • Detection and interpretation of expression quantitative trait loci (eQTL)
    • Michaelson JJ, Loguercio S, Beyer A, (2009) Detection and interpretation of expression quantitative trait loci (eQTL). Methods 48: 265-276.
    • (2009) Methods , vol.48 , pp. 265-276
    • Michaelson, J.J.1    Loguercio, S.2    Beyer, A.3
  • 8
    • 0000702165 scopus 로고
    • Mutual information functions versus correlation functions
    • Li W, (1990) Mutual information functions versus correlation functions. Journal of Statistical Physics 60: 823-837.
    • (1990) Journal of Statistical Physics , vol.60 , pp. 823-837
    • Li, W.1
  • 11
    • 84862158859 scopus 로고    scopus 로고
    • Associations between Ionomic Profile and Metabolic Abnormalities in Human Population
    • Sun L, Yu Y, Huang T, An P, Yu D, et al. (2012) Associations between Ionomic Profile and Metabolic Abnormalities in Human Population. PLoS One 7: e38845.
    • (2012) PLoS One , vol.7
    • Sun, L.1    Yu, Y.2    Huang, T.3    An, P.4    Yu, D.5
  • 12
    • 0016532771 scopus 로고
    • A Theory of Program Size Formally Identical to Information Theory
    • Chaitin GJ, (1975) A Theory of Program Size Formally Identical to Information Theory. Journal of the ACM 22: 329-340.
    • (1975) Journal of the ACM , vol.22 , pp. 329-340
    • Chaitin, G.J.1
  • 13
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • 623-656
    • Shannon CE (1948) A mathematical theory of communication. Bell System Technical Journal 27: 379-424, 623-656.
    • (1948) Bell System Technical Journal , vol.27 , pp. 379-424
    • Shannon, C.E.1
  • 16
    • 79953868412 scopus 로고    scopus 로고
    • Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma
    • Geng H, Iqbal J, Chan WC, Ali HH, (2011) Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma. BMC Med Genomics 4: 32.
    • (2011) BMC Med Genomics , vol.4 , pp. 32
    • Geng, H.1    Iqbal, J.2    Chan, W.C.3    Ali, H.H.4
  • 17
    • 84860329478 scopus 로고    scopus 로고
    • Bayesian method to predict individual SNP genotypes from gene expression data
    • Schadt EE, Woo S, Hao K, (2012) Bayesian method to predict individual SNP genotypes from gene expression data. Nat Genet 44: 603-608.
    • (2012) Nat Genet , vol.44 , pp. 603-608
    • Schadt, E.E.1    Woo, S.2    Hao, K.3
  • 18
    • 39049100407 scopus 로고    scopus 로고
    • Sex specific gene regulation and expression QTLs in mouse macrophages from a strain intercross
    • Bhasin JM, Chakrabarti E, Peng DQ, Kulkarni A, Chen X, et al. (2008) Sex specific gene regulation and expression QTLs in mouse macrophages from a strain intercross. PLoS One 3: e1435.
    • (2008) PLoS One , vol.3
    • Bhasin, J.M.1    Chakrabarti, E.2    Peng, D.Q.3    Kulkarni, A.4    Chen, X.5
  • 20
    • 84861153094 scopus 로고    scopus 로고
    • Matrix eQTL: ultra fast eQTL analysis via large matrix operations
    • Shabalin AA, (2012) Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28: 1353-1358.
    • (2012) Bioinformatics , vol.28 , pp. 1353-1358
    • Shabalin, A.A.1
  • 21
    • 33646541424 scopus 로고    scopus 로고
    • Atherosclerosis susceptibility loci identified from a strain intercross of apolipoprotein E-deficient mice via a high-density genome scan
    • Smith JD, Bhasin JM, Baglione J, Settle M, Xu Y, et al. (2006) Atherosclerosis susceptibility loci identified from a strain intercross of apolipoprotein E-deficient mice via a high-density genome scan. Arterioscler Thromb Vasc Biol 26: 597-603.
    • (2006) Arterioscler Thromb Vasc Biol , vol.26 , pp. 597-603
    • Smith, J.D.1    Bhasin, J.M.2    Baglione, J.3    Settle, M.4    Xu, Y.5
  • 22
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy
    • Peng H, Long F, Ding C, (2005) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 27: 1226-1238.
    • (2005) IEEE Trans Pattern Anal Mach Intell , vol.27 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 23
    • 17644384367 scopus 로고    scopus 로고
    • Minimum redundancy feature selection from microarray gene expression data
    • Ding C, Peng H, (2005) Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol 3: 185-205.
    • (2005) J Bioinform Comput Biol , vol.3 , pp. 185-205
    • Ding, C.1    Peng, H.2
  • 24
    • 84857449527 scopus 로고    scopus 로고
    • Predicting triplet of transcription factor - mediating enzyme - target gene by functional profiles
    • Huang T, Chen L, Liu X-J, Cai Y-D, (2011) Predicting triplet of transcription factor- mediating enzyme- target gene by functional profiles. Neurocomputing 74: 3677-3681.
    • (2011) Neurocomputing , vol.74 , pp. 3677-3681
    • Huang, T.1    Chen, L.2    Liu, X.-J.3    Cai, Y.-D.4
  • 25
    • 84862641013 scopus 로고    scopus 로고
    • Prediction of lysine ubiquitination with mRMR feature selection and analysis
    • Cai Y, Huang T, Hu L, Shi X, Xie L, et al. (2011) Prediction of lysine ubiquitination with mRMR feature selection and analysis. Amino Acids.
    • (2011) Amino Acids
    • Cai, Y.1    Huang, T.2    Hu, L.3    Shi, X.4    Xie, L.5
  • 26
    • 78649458939 scopus 로고    scopus 로고
    • Analysis of protein pathway networks using hybrid properties
    • Chen L, Huang T, Shi XH, Cai YD, Chou KC, (2010) Analysis of protein pathway networks using hybrid properties. Molecules 15: 8177-8192.
    • (2010) Molecules , vol.15 , pp. 8177-8192
    • Chen, L.1    Huang, T.2    Shi, X.H.3    Cai, Y.D.4    Chou, K.C.5
  • 28
    • 77949493376 scopus 로고    scopus 로고
    • Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles
    • Huang T, Cui W, Hu L, Feng K, Li YX, et al. (2009) Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS ONE 4: e8126.
    • (2009) PLoS ONE , vol.4
    • Huang, T.1    Cui, W.2    Hu, L.3    Feng, K.4    Li, Y.X.5
  • 29
    • 52749089141 scopus 로고    scopus 로고
    • The prediction of interferon treatment effects based on time series microarray gene expression profiles
    • Huang T, Tu K, Shyr Y, Wei CC, Xie L, et al. (2008) The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med 6: 44.
    • (2008) J Transl Med , vol.6 , pp. 44
    • Huang, T.1    Tu, K.2    Shyr, Y.3    Wei, C.C.4    Xie, L.5
  • 30
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition
    • Chou KC, (2011) Some remarks on protein attribute prediction and pseudo amino acid composition. J Theor Biol 273: 236-247.
    • (2011) J Theor Biol , vol.273 , pp. 236-247
    • Chou, K.C.1
  • 31
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou KC, Shen HB, (2007) Recent progress in protein subcellular location prediction. Anal Biochem 370: 1-16.
    • (2007) Anal Biochem , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 32
    • 84862792208 scopus 로고    scopus 로고
    • Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches
    • Huang T, Zhang J, Xu Z, Hu L, Chen L, et al. (2012) Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches. Biochimie.
    • (2012) Biochimie
    • Huang, T.1    Zhang, J.2    Xu, Z.3    Hu, L.4    Chen, L.5
  • 33
    • 79952350255 scopus 로고    scopus 로고
    • Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and the Virus-Host Interaction Network
    • Huang T, Xu Z, Chen L, Cai YD, Kong X, (2011) Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and the Virus-Host Interaction Network. PLoS ONE 6: e17291.
    • (2011) PLoS ONE , vol.6
    • Huang, T.1    Xu, Z.2    Chen, L.3    Cai, Y.D.4    Kong, X.5
  • 34
    • 79251548286 scopus 로고    scopus 로고
    • Analysis and prediction of translation rate based on sequence and functional features of the mRNA
    • Huang T, Wan S, Xu Z, Zheng Y, Feng KY, et al. (2011) Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS ONE 6: e16036.
    • (2011) PLoS ONE , vol.6
    • Huang, T.1    Wan, S.2    Xu, Z.3    Zheng, Y.4    Feng, K.Y.5
  • 35
    • 79961193016 scopus 로고    scopus 로고
    • Predicting Transcriptional Activity of Multiple Site p53 Mutants Based on Hybrid Properties
    • Huang T, Niu S, Xu Z, Huang Y, Kong X, et al. (2011) Predicting Transcriptional Activity of Multiple Site p53 Mutants Based on Hybrid Properties. PLoS ONE 6: e22940.
    • (2011) PLoS ONE , vol.6
    • Huang, T.1    Niu, S.2    Xu, Z.3    Huang, Y.4    Kong, X.5
  • 36
    • 80053220447 scopus 로고    scopus 로고
    • Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property
    • Huang T, Chen L, Cai YD, Chou KC, (2011) Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS ONE 6: e25297.
    • (2011) PLoS ONE , vol.6
    • Huang, T.1    Chen, L.2    Cai, Y.D.3    Chou, K.C.4
  • 37
    • 77955645823 scopus 로고    scopus 로고
    • Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties
    • Huang T, Wang P, Ye ZQ, Xu H, He Z, et al. (2010) Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties. PLoS ONE 5: e11900.
    • (2010) PLoS ONE , vol.5
    • Huang, T.1    Wang, P.2    Ye, Z.Q.3    Xu, H.4    He, Z.5
  • 38
    • 77955199287 scopus 로고    scopus 로고
    • Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
    • Huang T, Shi XH, Wang P, He Z, Feng KY, et al. (2010) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE 5: e10972.
    • (2010) PLoS ONE , vol.5
    • Huang, T.1    Shi, X.H.2    Wang, P.3    He, Z.4    Feng, K.Y.5
  • 39
    • 84894898597 scopus 로고    scopus 로고
    • SySAP: a system-level predictor of deleterious single amino acid polymorphisms
    • Huang T, Wang C, Zhang G, Xie L, Li Y (2011) SySAP: a system-level predictor of deleterious single amino acid polymorphisms. Protein Cell.
    • (2011) Protein Cell
    • Huang, T.1    Wang, C.2    Zhang, G.3    Xie, L.4    Li, Y.5
  • 40
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
    • (2011) Nucleic Acids Res , vol.39
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4    Roth, A.5
  • 41
    • 79951859668 scopus 로고    scopus 로고
    • The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma
    • Huang T, Liu L, Liu Q, Ding G, Tan Y, et al. (2011) The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. Int J Comput Biol Drug Des 4: 5-18.
    • (2011) Int J Comput Biol Drug Des , vol.4 , pp. 5-18
    • Huang, T.1    Liu, L.2    Liu, Q.3    Ding, G.4    Tan, Y.5
  • 42
    • 77954147517 scopus 로고    scopus 로고
    • Using GeneReg to construct time delay gene regulatory networks
    • Huang T, Liu L, Qian Z, Tu K, Li Y, et al. (2010) Using GeneReg to construct time delay gene regulatory networks. BMC Res Notes 3: 142.
    • (2010) BMC Res Notes , vol.3 , pp. 142
    • Huang, T.1    Liu, L.2    Qian, Z.3    Tu, K.4    Li, Y.5
  • 44
    • 84863283565 scopus 로고    scopus 로고
    • Selection of Reprogramming Factors of Induced Pluripotent Stem Cells Based on the Protein Interaction Network and Functional Profiles
    • Huang T, Cai YD, Chen L, Hu L, Kong XY, et al. (2011) Selection of Reprogramming Factors of Induced Pluripotent Stem Cells Based on the Protein Interaction Network and Functional Profiles. Protein Pept Lett.
    • (2011) Protein Pept Lett
    • Huang, T.1    Cai, Y.D.2    Chen, L.3    Hu, L.4    Kong, X.Y.5
  • 49
    • 84864197093 scopus 로고    scopus 로고
    • Teamwork: improved eQTL mapping using combinations of machine learning methods
    • Ackermann M, Clement-Ziza M, Michaelson JJ, Beyer A, (2012) Teamwork: improved eQTL mapping using combinations of machine learning methods. PLoS One 7: e40916.
    • (2012) PLoS One , vol.7
    • Ackermann, M.1    Clement-Ziza, M.2    Michaelson, J.J.3    Beyer, A.4
  • 50
    • 33745220961 scopus 로고    scopus 로고
    • A review of statistical methods for expression quantitative trait loci mapping
    • Kendziorski C, Wang P, (2006) A review of statistical methods for expression quantitative trait loci mapping. Mamm Genome 17: 509-517.
    • (2006) Mamm Genome , vol.17 , pp. 509-517
    • Kendziorski, C.1    Wang, P.2
  • 51
    • 35548987435 scopus 로고    scopus 로고
    • A statistical framework for expression quantitative trait loci mapping
    • Chen M, Kendziorski C, (2007) A statistical framework for expression quantitative trait loci mapping. Genetics 177: 761-771.
    • (2007) Genetics , vol.177 , pp. 761-771
    • Chen, M.1    Kendziorski, C.2
  • 52
    • 33645068841 scopus 로고    scopus 로고
    • Statistical methods for expression quantitative trait loci (eQTL) mapping
    • Kendziorski CM, Chen M, Yuan M, Lan H, Attie AD, (2006) Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62: 19-27.
    • (2006) Biometrics , vol.62 , pp. 19-27
    • Kendziorski, C.M.1    Chen, M.2    Yuan, M.3    Lan, H.4    Attie, A.D.5
  • 53


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