메뉴 건너뛰기




Volumn 31, Issue 19, 2015, Pages 3163-3171

Sparse multi-view matrix factorization: A multivariate approach to multiple tissue comparisons

Author keywords

[No Author keywords available]

Indexed keywords

ADIPOSE TISSUE; ADULT; ALGORITHM; ANTIBODY SPECIFICITY; CELL CULTURE; COHORT ANALYSIS; COMPARATIVE STUDY; CYTOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; LYMPHOCYTE; METABOLISM; PHENOTYPE; PROCEDURES; SKIN; TWINS;

EID: 84943406525     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv344     Document Type: Article
Times cited : (8)

References (45)
  • 1
    • 0037184265 scopus 로고    scopus 로고
    • Reduced expression and increased cpg dinucleotide methylation of the rat apobec-1 promoter in transgenic rabbits
    • Apostel, F. et al. (2002) Reduced expression and increased cpg dinucleotide methylation of the rat apobec-1 promoter in transgenic rabbits. Biochim. Biophys. Acta, 1577, 384-394
    • (2002) Biochim. Biophys. Acta , vol.1577 , pp. 384-394
    • Apostel, F.1
  • 2
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 3
    • 84860572791 scopus 로고    scopus 로고
    • Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population
    • Bell, J. et al. (2012) Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet., 8, e1002629
    • (2012) PLoS Genet , vol.8 , pp. e1002629
    • Bell, J.1
  • 4
    • 0033569724 scopus 로고    scopus 로고
    • Purification molecular cloning, and expression of a human stratum corneum trypsin-like serine protease with possible function in desquamation
    • Brattsand, M. and Egelrud, T. (1999) Purification, molecular cloning, and expression of a human stratum corneum trypsin-like serine protease with possible function in desquamation. J. Biol. Chem., 274, 30033-30040
    • (1999) J. Biol. Chem , vol.274 , pp. 30033-30040
    • Brattsand, M.1    Egelrud, T.2
  • 5
    • 0037370311 scopus 로고    scopus 로고
    • Natural variation in human gene expression assessed in lymphoblastoid cells
    • Cheung, V. et al. (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet., 33, 422-425
    • (2003) Nat. Genet , vol.33 , pp. 422-425
    • Cheung, V.1
  • 6
    • 84874967142 scopus 로고    scopus 로고
    • Identification of seven loci affecting mean telomere length and their association with disease
    • Codd, V. et al. (2013) Identification of seven loci affecting mean telomere length and their association with disease. Nat. Genet., 45, 422-427
    • (2013) Nat. Genet , vol.45 , pp. 422-427
    • Codd, V.1
  • 7
    • 84880920116 scopus 로고    scopus 로고
    • Eukaryotic transcriptional dynamics: From single molecules to cell populations
    • Coulon, A. et al. (2013) Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat. Rev. Genet., 14, 572-584
    • (2013) Nat. Rev. Genet , vol.14 , pp. 572-584
    • Coulon, A.1
  • 8
    • 67349286456 scopus 로고    scopus 로고
    • Development of an ichthyosiform phenotype in alox12b-deficient mouse skin transplants
    • De Juanes, S. et al. (2009) Development of an ichthyosiform phenotype in alox12b-deficient mouse skin transplants. J. Invest. Dermatol., 129, 1429-1436
    • (2009) J. Invest. Dermatol , vol.129 , pp. 1429-1436
    • De Juanes, S.1
  • 9
    • 45849107328 scopus 로고    scopus 로고
    • Pathwise coordinate optimization
    • Friedman, J. et al. (2007) Pathwise coordinate optimization. Ann. Appl. Stat., 2, 302-332
    • (2007) Ann. Appl. Stat , vol.2 , pp. 302-332
    • Friedman, J.1
  • 10
    • 77955140508 scopus 로고    scopus 로고
    • The impact of Levene's test of equality of variances on statistical theory and practice
    • Gastwirth, J. et al. (2009) The impact of Levene's test of equality of variances on statistical theory and practice. Stat. Sci., 24, 343-360
    • (2009) Stat. Sci , vol.24 , pp. 343-360
    • Gastwirth, J.1
  • 11
    • 84880940121 scopus 로고    scopus 로고
    • Gene expression changes with age in skin, adipose tissue, blood and brain
    • Glass, D. et al. (2013) Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol., 14, R75
    • (2013) Genome Biol , vol.14 , pp. R75
    • Glass, D.1
  • 12
    • 36348960733 scopus 로고    scopus 로고
    • Biconvex sets and optimization with biconvex functions: A survey and extensions
    • Gorski, J. et al. (2007) Biconvex sets and optimization with biconvex functions: a survey and extensions. Math Methods Oper. Res., 66, 373-401
    • (2007) Math Methods Oper. Res , vol.66 , pp. 373-401
    • Gorski, J.1
  • 13
    • 84866871814 scopus 로고    scopus 로고
    • Mapping cis- and trans-regulatory effects across multiple tissues in twins
    • Grundberg, E. et al. (2012) Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat. Genet., 44, 1084-1089
    • (2012) Nat. Genet , vol.44 , pp. 1084-1089
    • Grundberg, E.1
  • 14
    • 46249103142 scopus 로고    scopus 로고
    • Differential variability analysis of gene expression and its application to human diseases
    • Ho, J. et al. (2008) Differential variability analysis of gene expression and its application to human diseases. Bioinformatics, 24, 390-398
    • (2008) Bioinformatics , vol.24 , pp. 390-398
    • Ho, J.1
  • 15
    • 22244475458 scopus 로고    scopus 로고
    • An atlas of human gene expression from massively parallel signature sequencing (mpss)
    • Jongeneel, C. et al. (2005) An atlas of human gene expression from massively parallel signature sequencing (mpss). Genome Res., 15, 1007-1014
    • (2005) Genome Res , vol.15 , pp. 1007-1014
    • Jongeneel, C.1
  • 16
    • 85023633373 scopus 로고
    • Complete protein sequence and identification of structural domains of human apolipoprotein b.
    • Knott, T. et al. (1986) Complete protein sequence and identification of structural domains of human apolipoprotein b. Nature, 323, 134-138
    • (1986) Nature , vol.323 , pp. 134-138
    • Knott, T.1
  • 17
    • 58549101103 scopus 로고    scopus 로고
    • A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
    • Lage, K. et al. (2008) A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc. Natl. Acad. Sci. USA., 105, 20870-20875
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 20870-20875
    • Lage, K.1
  • 18
    • 78049444975 scopus 로고    scopus 로고
    • Gene expression variability within and between human populations and implications toward disease susceptibility
    • Li, J. et al. (2010) Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput. Biol., 6, e1000910
    • (2010) PLoS Comput. Biol , vol.6 , pp. e1000910
    • Li, J.1
  • 19
    • 46049110099 scopus 로고    scopus 로고
    • Tiger: A database for tissue-specific gene expression and regulation
    • Liu, X. et al. (2008) Tiger: a database for tissue-specific gene expression and regulation. BMC Bioinformatics, 9, 271
    • (2008) BMC Bioinformatics , vol.9 , pp. 271
    • Liu, X.1
  • 20
    • 84899630492 scopus 로고    scopus 로고
    • DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
    • Lokk, K. et al. (2014) DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biol., 15, r54
    • (2014) Genome Biol , vol.15 , pp. r54
    • Lokk, K.1
  • 21
    • 79952109284 scopus 로고    scopus 로고
    • The relationship between methylation of the syk gene in the promoter region and the genesis of lung cancer
    • Ma, L. et al. (2010) The relationship between methylation of the syk gene in the promoter region and the genesis of lung cancer. Clin. Lab., 56, 407-416
    • (2010) Clin. Lab , vol.56 , pp. 407-416
    • Ma, L.1
  • 22
    • 49949090353 scopus 로고    scopus 로고
    • Penalized feature selection and classification in bioinformatics
    • Ma, S. and Huang, J. (2008) Penalized feature selection and classification in bioinformatics. Brief. Bioinform., 9, 392-403
    • (2008) Brief. Bioinform , vol.9 , pp. 392-403
    • Ma, S.1    Huang, J.2
  • 23
    • 80052308980 scopus 로고    scopus 로고
    • Variance of gene expression identifies altered network constraints in neurological diseases
    • Mar, J. et al. (2011) Variance of gene expression identifies altered network constraints in neurological diseases. PLoS Genet., 7, e1002207
    • (2011) PLoS Genet , vol.7 , pp. e1002207
    • Mar, J.1
  • 25
    • 84875631900 scopus 로고    scopus 로고
    • Cohort profile: Twinsuk and healthy ageing twin study
    • Moayyeri, A. et al. (2013) Cohort profile: Twinsuk and healthy ageing twin study. Int. J. Epidemiol., 42, 76-85
    • (2013) Int. J. Epidemiol , vol.42 , pp. 76-85
    • Moayyeri, A.1
  • 26
    • 79952256739 scopus 로고    scopus 로고
    • The architecture of gene regulatory variation across multiple human tissues: The MuTHER study
    • Nica, A. et al. (2011) The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet., 7, e1002003
    • (2011) PLoS Genet , vol.7 , pp. e1002003
    • Nica, A.1
  • 27
    • 79952901680 scopus 로고    scopus 로고
    • Enhancer function: New insights into the regulation of tissue-specific gene expression
    • Ong, C.-T. and Corces, V. (2011) Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat. Rev. Genet., 12, 283-293
    • (2011) Nat. Rev. Genet , vol.12 , pp. 283-293
    • Ong, C.-T.1    Corces, V.2
  • 28
    • 85023626473 scopus 로고    scopus 로고
    • A higher-order generalized singular value decomposition for comparison of global mRNA expression from multiple organisms
    • Ponnapalli, S.P. et al. (2011) A higher-order generalized singular value decomposition for comparison of global mRNA expression from multiple organisms. PLoS One, 6, 1-11
    • (2011) PLoS One , vol.6 , pp. 1-11
    • Ponnapalli, S.P.1
  • 29
    • 0025945632 scopus 로고
    • DNA methylation and gene expression
    • Razin, A. and Cedar, H. (1991) DNA methylation and gene expression. Microbiol. Mol. Biol. Rev., 55, 451-458
    • (1991) Microbiol. Mol. Biol. Rev , vol.55 , pp. 451-458
    • Razin, A.1    Cedar, H.2
  • 30
    • 34249279527 scopus 로고    scopus 로고
    • Stability and flexibility of epigenetic gene regulation in mammalian development
    • Reik, W. (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature, 447, 425-432
    • (2007) Nature , vol.447 , pp. 425-432
    • Reik, W.1
  • 31
    • 0033320633 scopus 로고    scopus 로고
    • Reduction in visceral adipose tissue is associated with improvement in apolipoprotein b-100 metabolism in obese men
    • Riches, F. et al. (1999) Reduction in visceral adipose tissue is associated with improvement in apolipoprotein b-100 metabolism in obese men. J. Clin. Endocrinol. Metab., 84, 2854-2861
    • (1999) J. Clin. Endocrinol. Metab , vol.84 , pp. 2854-2861
    • Riches, F.1
  • 32
    • 84869054051 scopus 로고    scopus 로고
    • A travel guide to cytoscape plugins
    • Saito, R. et al. (2012) A travel guide to cytoscape plugins. Nat. Methods, 9, 1069-1076
    • (2012) Nat. Methods , vol.9 , pp. 1069-1076
    • Saito, R.1
  • 33
    • 65849518449 scopus 로고    scopus 로고
    • Utility of lymphoblastoid cell lines
    • Sie, L. et al. (2009) Utility of lymphoblastoid cell lines. J. Neurosci. Res., 87, 1953-1959
    • (2009) J. Neurosci. Res , vol.87 , pp. 1953-1959
    • Sie, L.1
  • 34
    • 33748992313 scopus 로고    scopus 로고
    • Adipocytokines:mediators linking adipose tissue inflammation and immunity
    • Tilg, H. and Moschen, A. (2006) Adipocytokines:mediators linking adipose tissue, inflammation and immunity. Nat. Rev. Immunol., 6, 772-783
    • (2006) Nat. Rev. Immunol , vol.6 , pp. 772-783
    • Tilg, H.1    Moschen, A.2
  • 35
    • 0002196917 scopus 로고
    • Comparing individual means in the analysis of variance
    • Tukey, J. (1949) Comparing individual means in the analysis of variance. Biometrics, 5, 99-114
    • (1949) Biometrics , vol.5 , pp. 99-114
    • Tukey, J.1
  • 36
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • Van't Veer, L. et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536
    • (2002) Nature , vol.415 , pp. 530-536
    • Van'T Veer, L.1
  • 37
    • 84906979420 scopus 로고    scopus 로고
    • Epigenome-wide DNA methylation in hearing ability: New mechanisms for an old problem
    • Wolber, L. et al. (2014) Epigenome-wide DNA methylation in hearing ability: new mechanisms for an old problem. PLoS One, 9, e105729
    • (2014) PLoS One , vol.9 , pp. e105729
    • Wolber, L.1
  • 38
    • 73849105202 scopus 로고    scopus 로고
    • Combinatorial control of suicide gene expression by tissue-specific promoter and microRNA regulation for cancer therapy
    • Wu, C. et al. (2009) Combinatorial control of suicide gene expression by tissue-specific promoter and microRNA regulation for cancer therapy. Mol. Ther., 17, 2058-2066
    • (2009) Mol. Ther , vol.17 , pp. 2058-2066
    • Wu, C.1
  • 39
    • 84907437678 scopus 로고    scopus 로고
    • Tissue-specific RNA expression marks distant-acting developmental enhancers
    • Wu, H. et al. (2014) Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet., 10, e1004610
    • (2014) PLoS Genet , vol.10 , pp. e1004610
    • Wu, H.1
  • 40
    • 39649103085 scopus 로고    scopus 로고
    • Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm Bombyx mori
    • Xia, Q. et al. (2007) Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm Bombyx mori. Genome Biol., 8, R162
    • (2007) Genome Biol , vol.8 , pp. R162
    • Xia, Q.1
  • 41
    • 84896722835 scopus 로고    scopus 로고
    • Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules
    • Xiao, X. et al. (2014) Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules. PLoS Genet., 10, e1004006
    • (2014) PLoS Genet , vol.10 , pp. e1004006
    • Xiao, X.1
  • 42
    • 79955780589 scopus 로고    scopus 로고
    • Verygene: Linking tissue-specific genes to diseases drugs, and beyond for knowledge discovery
    • Yang, X. et al. (2011) Verygene: linking tissue-specific genes to diseases, drugs, and beyond for knowledge discovery. Physiol. Genomics, 43, 457-460
    • (2011) Physiol. Genomics , vol.43 , pp. 457-460
    • Yang, X.1
  • 43
    • 32444442875 scopus 로고    scopus 로고
    • RNAs induced by Epstein-Barr virus nuclear antigen 2 in lymphoblastoid cell lines
    • Zhao, B. et al. (2006) RNAs induced by Epstein-Barr virus nuclear antigen 2 in lymphoblastoid cell lines. Proc. Natl. Acad. Sci. USA., 103, 1900-1905
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1900-1905
    • Zhao, B.1
  • 44
    • 84882884517 scopus 로고    scopus 로고
    • Charting a dynamic DNA methylation landscape of the human genome
    • Ziller, M. et al. (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature, 500, 477-481
    • (2013) Nature , vol.500 , pp. 477-481
    • Ziller, M.1
  • 45
    • 33745309913 scopus 로고    scopus 로고
    • Sparse principal component analysis
    • Zou, H. et al. (2006) Sparse principal component analysis. J. Comput. Graph. Stat., 15, 265-286
    • (2006) J. Comput. Graph. Stat , vol.15 , pp. 265-286
    • Zou, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.