메뉴 건너뛰기




Volumn 7, Issue 12, 2012, Pages

Simultaneous Non-Negative Matrix Factorization for Multiple Large Scale Gene Expression Datasets in Toxicology

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE AMINOTRANSFERASE; ASPARTATE AMINOTRANSFERASE; CREATINE KINASE; CREATININE; LACTATE DEHYDROGENASE; NITROGEN; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR AGONIST; PPM 201; UNCLASSIFIED DRUG; UREA;

EID: 84871305336     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048238     Document Type: Article
Times cited : (18)

References (37)
  • 1
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negative matrix factorization
    • Lee DD, Seung HS, (1999) Learning the parts of objects by non-negative matrix factorization. Nature 401: 788-791.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 3
    • 1642529511 scopus 로고    scopus 로고
    • Metagenes and molecular pattern discovery using matrix factorisation
    • Brunet JP, Tamayo P, Golub TR, Mesirov JP, (2004) Metagenes and molecular pattern discovery using matrix factorisation. Proc Nat Acad Sci 101: 4164-4169.
    • (2004) Proc Nat Acad Sci , vol.101 , pp. 4164-4169
    • Brunet, J.P.1    Tamayo, P.2    Golub, T.R.3    Mesirov, J.P.4
  • 4
    • 33845903308 scopus 로고    scopus 로고
    • Inferential, robust non-negative matrix factorization analysis of microarray data
    • Fogel P, Young SS, Hawkins DM, Ledirac N, (2007) Inferential, robust non-negative matrix factorization analysis of microarray data. Bioinformatics 23: 44-49.
    • (2007) Bioinformatics , vol.23 , pp. 44-49
    • Fogel, P.1    Young, S.S.2    Hawkins, D.M.3    Ledirac, N.4
  • 5
    • 34547844077 scopus 로고    scopus 로고
    • Sparse non-negative matrix factorizations via alternating non-negativityconstrained least squares for microarray data analysis
    • Kim H, Park H, (2007) Sparse non-negative matrix factorizations via alternating non-negativityconstrained least squares for microarray data analysis. Bioinformatics 23: 1495-1502.
    • (2007) Bioinformatics , vol.23 , pp. 1495-1502
    • Kim, H.1    Park, H.2
  • 7
    • 27744601822 scopus 로고    scopus 로고
    • Improving molecular cancer class discovery through sparse non-negative matrix factorization
    • Gao Y, Church G, (2005) Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 21: 3970-3975.
    • (2005) Bioinformatics , vol.21 , pp. 3970-3975
    • Gao, Y.1    Church, G.2
  • 8
    • 48249151183 scopus 로고    scopus 로고
    • Nonnegative matrix factorization: An analytical and interpretive tool in computational biology
    • Devarajan K, (2008) Nonnegative matrix factorization: An analytical and interpretive tool in computational biology. PLoS Comput Biol 4: e1000029.
    • (2008) PLoS Comput Biol , vol.4
    • Devarajan, K.1
  • 9
    • 77949611040 scopus 로고    scopus 로고
    • Combining gene expression and transcription factor regulation data using simultaneous nonnegative matrix factorization
    • BIOCOMP-2007
    • Badea L (2007) Combining gene expression and transcription factor regulation data using simultaneous nonnegative matrix factorization. In: Proc. BIOCOMP-2007. pp. 127-131.
    • (2007) Proc , pp. 127-131
    • Badea, L.1
  • 10
    • 40549140784 scopus 로고    scopus 로고
    • Extracting gene expression profiles common to colon and pancreatic adenocarcinoma using simultaneous nonnegative matrix factorization
    • Pacific Symposium on Biocomputing PSB-2008
    • Badea L (2008) Extracting gene expression profiles common to colon and pancreatic adenocarcinoma using simultaneous nonnegative matrix factorization. In: Proc. Pacific Symposium on Biocomputing PSB-2008. pp. 267-278.
    • (2008) Proc , pp. 267-278
    • Badea, L.1
  • 12
    • 77956335013 scopus 로고    scopus 로고
    • Potential remains for PPAR-targeted drugs
    • Jones D, (2010) Potential remains for PPAR-targeted drugs. Nature Reviews Drug Discovery 9: 668-669.
    • (2010) Nature Reviews Drug Discovery , vol.9 , pp. 668-669
    • Jones, D.1
  • 13
    • 84898964201 scopus 로고    scopus 로고
    • Algorithms for non-negative matrix factorization
    • Lee DD, Seung HS, (2001) Algorithms for non-negative matrix factorization. Adv Neural Info Proc Syst 13: 556-562.
    • (2001) Adv Neural Info Proc Syst , vol.13 , pp. 556-562
    • Lee, D.D.1    Seung, H.S.2
  • 14
    • 0038724494 scopus 로고    scopus 로고
    • Consensus clustering: a resampling-basedmethod for class discovery and visualization of gene expression microarray data
    • Monit S, Tamayo P, Mesirov J, Golub T, (2003) Consensus clustering: a resampling-basedmethod for class discovery and visualization of gene expression microarray data. Machine Learning 52: 91-118.
    • (2003) Machine Learning , vol.52 , pp. 91-118
    • Monit, S.1    Tamayo, P.2    Mesirov, J.3    Golub, T.4
  • 15
    • 0002789875 scopus 로고    scopus 로고
    • Principles of clinical pathology for toxicology studies
    • Taylor and Francis, Philadelphia, 4th edition
    • Hall R (2001) Principles of clinical pathology for toxicology studies. In Principles and methods of toxicology. Taylor and Francis, Philadelphia, 4th edition.
    • (2001) Principles and methods of toxicology
    • Hall, R.1
  • 16
    • 33846407232 scopus 로고    scopus 로고
    • Apolipoprotein A1 is a stronger prognostic marker than are HDL and LDL cholesterol for cardiovascular disease and mortality in elderly men
    • Florvall G, Basu S, Larsson A, (2006) Apolipoprotein A1 is a stronger prognostic marker than are HDL and LDL cholesterol for cardiovascular disease and mortality in elderly men. The Journals of Gerontology Series A, Biological Sciences and Medical Sciences 61: 1262-1266.
    • (2006) The Journals of Gerontology Series A, Biological Sciences and Medical Sciences , vol.61 , pp. 1262-1266
    • Florvall, G.1    Basu, S.2    Larsson, A.3
  • 17
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc 4: 44-57.
    • (2009) Nature Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 19
  • 20
    • 0030770826 scopus 로고    scopus 로고
    • Complex formation between junctin, triadin, calsequestrin, and the ryanodine receptor. proteins of the cardiac junctional sarcoplasmic reticulum membrane
    • Zhang L, Kelley J, Schmeisser G, Kobayashi YM, Jones LR, (1997) Complex formation between junctin, triadin, calsequestrin, and the ryanodine receptor. proteins of the cardiac junctional sarcoplasmic reticulum membrane. J Biol Chem pp. 23389-97.
    • (1997) J Biol Chem , pp. 23389-23397
    • Zhang, L.1    Kelley, J.2    Schmeisser, G.3    Kobayashi, Y.M.4    Jones, L.R.5
  • 21
    • 41149149804 scopus 로고    scopus 로고
    • Isoform diversity, regulation, and functional adaptation of troponin and calponin
    • Jin J, Zhang Z, Bautista J, (2008) Isoform diversity, regulation, and functional adaptation of troponin and calponin. Crit Rev Eukaryot Gene Expr 18: 93-124.
    • (2008) Crit Rev Eukaryot Gene Expr , vol.18 , pp. 93-124
    • Jin, J.1    Zhang, Z.2    Bautista, J.3
  • 22
    • 0025142936 scopus 로고
    • The structure and regulation of expression of the murine fast skeletal troponin c gene. identification of a developmentally regulated, muscle-specific transcriptional enhancer
    • Parmacek M, Bengur A, Vora A, Leiden J, (1990) The structure and regulation of expression of the murine fast skeletal troponin c gene. identification of a developmentally regulated, muscle-specific transcriptional enhancer. J Biol Chem 265: 15970-6.
    • (1990) J Biol Chem , vol.265 , pp. 15970-15976
    • Parmacek, M.1    Bengur, A.2    Vora, A.3    Leiden, J.4
  • 23
    • 0029031198 scopus 로고
    • The troponin complex and regulation of muscle contraction
    • Farah C, Reinach F, (1995) The troponin complex and regulation of muscle contraction. FASEB J 9: 755-67.
    • (1995) FASEB J , vol.9 , pp. 755-767
    • Farah, C.1    Reinach, F.2
  • 24
    • 0742289174 scopus 로고    scopus 로고
    • What is the role of tropomyosin in the regulation of muscle contraction?
    • Perry S, (2003) What is the role of tropomyosin in the regulation of muscle contraction? J Muscle Res Cell Motil 24: 593-6.
    • (2003) J Muscle Res Cell Motil , vol.24 , pp. 593-596
    • Perry, S.1
  • 25
    • 15544390385 scopus 로고    scopus 로고
    • Calcium, thin filaments, and the integrative biology of cardiac contractility
    • Kobayashi T, Solaro R, (2005) Calcium, thin filaments, and the integrative biology of cardiac contractility. Annu Rev Physiol 67: 39-67.
    • (2005) Annu Rev Physiol , vol.67 , pp. 39-67
    • Kobayashi, T.1    Solaro, R.2
  • 26
    • 33845573067 scopus 로고    scopus 로고
    • Coordinated control of bile acids and lipogenesis through fxr-dependent regulation of fatty acid synthase
    • Matsukuma K, Bennett M, Huang J, Wang L, Gil G, et al. (2006) Coordinated control of bile acids and lipogenesis through fxr-dependent regulation of fatty acid synthase. J Lipid Res 47: 2754-61.
    • (2006) J Lipid Res , vol.47 , pp. 2754-2761
    • Matsukuma, K.1    Bennett, M.2    Huang, J.3    Wang, L.4    Gil, G.5
  • 27
    • 35648938666 scopus 로고    scopus 로고
    • Bile acids and their signaling pathways: eclectic regulators of diverse cellular functions
    • Scotti E, Gilardi F, Godio C, Gers E, Krneta J, et al. (2007) Bile acids and their signaling pathways: eclectic regulators of diverse cellular functions. Cell Mol Life Sci 64: 2477-91.
    • (2007) Cell Mol Life Sci , vol.64 , pp. 2477-2491
    • Scotti, E.1    Gilardi, F.2    Godio, C.3    Gers, E.4    Krneta, J.5
  • 28
    • 77952673509 scopus 로고    scopus 로고
    • Bile acids and their nuclear receptor fxr: Relevance for hepatobiliary and gastrointestinal disease
    • Gadaleta R, van Mil S, Oldenburg B, Siersema P, Klomp L, et al. (2010) Bile acids and their nuclear receptor fxr: Relevance for hepatobiliary and gastrointestinal disease. Biochim Biophys Acta 1801: 683-92.
    • (2010) Biochim Biophys Acta , vol.1801 , pp. 683-692
    • Gadaleta, R.1    van Mil, S.2    Oldenburg, B.3    Siersema, P.4    Klomp, L.5
  • 29
    • 0242349197 scopus 로고    scopus 로고
    • Regulation of hepatic fasting response by ppargamma coactivator - 1alpha (pgc-1): Requirement for hepatocyte nuclear factor 4alpha in gluconeogenesis
    • Rhee J, Inoue Y, Yoon J, Puigserver P, Fan M, et al. (2003) Regulation of hepatic fasting response by ppargamma coactivator- 1alpha (pgc-1): Requirement for hepatocyte nuclear factor 4alpha in gluconeogenesis. Proc Natl Acad Sci USA 100: 4012-7.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 4012-4017
    • Rhee, J.1    Inoue, Y.2    Yoon, J.3    Puigserver, P.4    Fan, M.5
  • 30
    • 0035823551 scopus 로고    scopus 로고
    • Negative regulation of human fibrinogen gene expression by peroxisome proliferator-activated receptor alpha agonists via inhibition of CCAAT box/enhancer-binding protein beta
    • Gervois P, Vu-Dac N, Kleemann R, Kockx M, Dubois G, et al. (2001) Negative regulation of human fibrinogen gene expression by peroxisome proliferator-activated receptor alpha agonists via inhibition of CCAAT box/enhancer-binding protein beta. J Biol Chem 276: 33471-7.
    • (2001) J Biol Chem , vol.276 , pp. 33471-33477
    • Gervois, P.1    Vu-Dac, N.2    Kleemann, R.3    Kockx, M.4    Dubois, G.5
  • 31
    • 0037232425 scopus 로고    scopus 로고
    • Myocardial damage, inflammation and thrombin inhibition in unstable coronary artery disease
    • R L
    • Oldgren J, Wallentin L, Grip L, R L, Nørgaard BL, et al. (2003) Myocardial damage, inflammation and thrombin inhibition in unstable coronary artery disease. EurHeart J 24: 86-93.
    • (2003) EurHeart J , vol.24 , pp. 86-93
    • Oldgren, J.1    Wallentin, L.2    Grip, L.3    Nørgaard, B.L.4
  • 32
    • 0028095919 scopus 로고
    • The acute phase response
    • Baumann H, Gauldie J, (1994) The acute phase response. Immunol Today 15: 74-80.
    • (1994) Immunol Today , vol.15 , pp. 74-80
    • Baumann, H.1    Gauldie, J.2
  • 33
    • 84871339415 scopus 로고    scopus 로고
    • Nuclear receptors in the regulation of lipid metabolism
    • T M
    • T M, (2010) Nuclear receptors in the regulation of lipid metabolism. Curr Cardio Risk Rep 4: 142-149.
    • (2010) Curr Cardio Risk Rep , vol.4 , pp. 142-149
  • 34
    • 0028321529 scopus 로고
    • Differential expression and activation of a family of murine peroxisome proliferator-activated receptors
    • Kliewer SA, Forman BM, Blumberg B, Ong ES, Borgmeyer U, et al. (1994) Differential expression and activation of a family of murine peroxisome proliferator-activated receptors. Proc Natl Acad Sci, U S A 91: 7355-9.
    • (1994) Proc Natl Acad Sci, U S A , vol.91 , pp. 7355-7359
    • Kliewer, S.A.1    Forman, B.M.2    Blumberg, B.3    Ong, E.S.4    Borgmeyer, U.5
  • 35
    • 0026517010 scopus 로고
    • Control of the peroxisomal beta-oxidation pathway by a novel family of nuclear hormone receptors
    • Dreyer C, Krey G, Keller H, Givel F, Helftenbein G, et al. (1992) Control of the peroxisomal beta-oxidation pathway by a novel family of nuclear hormone receptors. Cell 68: 879-87.
    • (1992) Cell , vol.68 , pp. 879-887
    • Dreyer, C.1    Krey, G.2    Keller, H.3    Givel, F.4    Helftenbein, G.5
  • 36
    • 33947226779 scopus 로고    scopus 로고
    • Underlying mechanisms of pharmacology and toxicity of a novel ppar agonist revealed using rodent and canine hepatocytes
    • Guo Y, Jolly R, Halstead B, Baker T, Stutz J, et al. (2007) Underlying mechanisms of pharmacology and toxicity of a novel ppar agonist revealed using rodent and canine hepatocytes. Toxicol Sci 96: 294-309.
    • (2007) Toxicol Sci , vol.96 , pp. 294-309
    • Guo, Y.1    Jolly, R.2    Halstead, B.3    Baker, T.4    Stutz, J.5
  • 37
    • 0034713444 scopus 로고    scopus 로고
    • Roles of PPARs in health and disease
    • Kersten S, Desvergne B, Wahli W, (2000) Roles of PPARs in health and disease. Nature 405: 421-4.
    • (2000) Nature , vol.405 , pp. 421-424
    • Kersten, S.1    Desvergne, B.2    Wahli, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.