메뉴 건너뛰기




Volumn 11, Issue 8, 2012, Pages 4120-4131

Bayesian independent component analysis recovers pathway signatures from blood metabolomics data

Author keywords

Bayesian; bioinformatics; blood serum; independent component analysis; metabolomics; population cohorts; systems biology

Indexed keywords

AMINO ACID; HIGH DENSITY LIPOPROTEIN;

EID: 84864595849     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300231n     Document Type: Article
Times cited : (23)

References (50)
  • 1
    • 33646595378 scopus 로고    scopus 로고
    • The Cinderella story of metabolic profiling: Does metabolomics get to go to the functional genomics ball?
    • DOI 10.1098/rstb.2005.1734
    • Griffin, J. L. The cinderella story of metabolic profiling: does metabolomics get to go to the functional genomics ball? Philos. Trans. R. Soc.,B 2006, 361 (1465) 147-161 (Pubitemid 44858949)
    • (2006) Philosophical Transactions of the Royal Society B: Biological Sciences , vol.361 , Issue.1465 , pp. 147-161
    • Griffin, J.L.1
  • 4
    • 80052249990 scopus 로고    scopus 로고
    • Metabolic profiling of diabetes: From black-box epidemiology to systems epidemiology
    • Hu, F. B. Metabolic profiling of diabetes: From black-box epidemiology to systems epidemiology Clin. Chem. 2011, 57 (9) 1224-1226
    • (2011) Clin. Chem. , vol.57 , Issue.9 , pp. 1224-1226
    • Hu, F.B.1
  • 5
    • 77956780120 scopus 로고    scopus 로고
    • Measurement of dietary exposure: A challenging problem which may be overcome thanks to metabolomics?
    • Fav, G.; Beckmann, M. E.; Draper, J. H.; Mathers, J. C. Measurement of dietary exposure: A challenging problem which may be overcome thanks to metabolomics? Genes Nutr. 2009, 4 (2) 135-141
    • (2009) Genes Nutr. , vol.4 , Issue.2 , pp. 135-141
    • Fav, G.1    Beckmann, M.E.2    Draper, J.H.3    Mathers, J.C.4
  • 6
    • 80054098422 scopus 로고    scopus 로고
    • Postprandial differences in the plasma metabolome of healthy finnish subjects after intake of a sourdough fermented endosperm rye bread versus white wheat bread
    • Bondia-Pons, I.; Nordlund, E.; Mattila, I.; Katina, K.; Aura, A. M.; Kolehmainen, M.; Oresic, M.; Mykkanen, H.; Poutanen, K. Postprandial differences in the plasma metabolome of healthy finnish subjects after intake of a sourdough fermented endosperm rye bread versus white wheat bread Nutr. J. 2011, 10 (1) 116
    • (2011) Nutr. J. , vol.10 , Issue.1 , pp. 116
    • Bondia-Pons, I.1    Nordlund, E.2    Mattila, I.3    Katina, K.4    Aura, A.M.5    Kolehmainen, M.6    Oresic, M.7    Mykkanen, H.8    Poutanen, K.9
  • 7
    • 77951125481 scopus 로고    scopus 로고
    • Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
    • Fendt, S. M.; Buescher, J. M.; Rudroff, F.; Picotti, P.; Zamboni, N.; Sauer, U. Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity Mol. Syst. Biol. 2010, 6, 356
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 356
    • Fendt, S.M.1    Buescher, J.M.2    Rudroff, F.3    Picotti, P.4    Zamboni, N.5    Sauer, U.6
  • 8
    • 80052242132 scopus 로고    scopus 로고
    • Targeting cancer metabolism: A therapeutic window opens
    • Heiden, M. G. V. Targeting cancer metabolism: a therapeutic window opens Nat. Rev. Drug Discovery 2011, 10 (9) 671-684
    • (2011) Nat. Rev. Drug Discovery , vol.10 , Issue.9 , pp. 671-684
    • Heiden, M.G.V.1
  • 9
    • 46349084465 scopus 로고    scopus 로고
    • Bioinformatics analysis of targeted metabolomics - Uncovering old and new tales of diabetic mice under medication
    • DOI 10.1210/en.2007-1747
    • Altmaier, E.; Ramsay, S. L.; Graber, A.; Mewes, H. W.; Weinberger, K. M.; Suhre, K. Bioinformatics analysis of targeted metabolomics-uncovering old and new tales of diabetic mice under medication Endocrinology 2008, 149 (7) 3478-3489 (Pubitemid 351919596)
    • (2008) Endocrinology , vol.149 , Issue.7 , pp. 3478-3489
    • Altmaier, E.1    Ramsay, S.L.2    Graber, A.3    Mewes, H.-W.4    Weinberger, K.M.5    Suhre, K.6
  • 14
    • 27944506780 scopus 로고    scopus 로고
    • Systems Neurobiology Laboratory, Salk Institute for Biological Studies: La Jolla, CA
    • Shlens, J. A Tutorial on Principal Component Analysis; Systems Neurobiology Laboratory, Salk Institute for Biological Studies: La Jolla, CA, 2005.
    • (2005) A Tutorial on Principal Component Analysis
    • Shlens, J.1
  • 15
    • 79251567361 scopus 로고    scopus 로고
    • Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
    • Krumsiek, J.; Suhre, K.; Illig, T.; Adamski, J.; Theis, F. J. Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data BMC Syst. Biol. 2011, 5 (1) 21
    • (2011) BMC Syst. Biol. , vol.5 , Issue.1 , pp. 21
    • Krumsiek, J.1    Suhre, K.2    Illig, T.3    Adamski, J.4    Theis, F.J.5
  • 16
    • 1642468351 scopus 로고    scopus 로고
    • Adaptive and learning systems for signal processing, communications, and control
    • J. Wiley: New York
    • Hyvärinen, A.; Karhunen, J.; Oja, E. Adaptive and learning systems for signal processing, communications, and control. Independent Component Analysis; J. Wiley: New York, 2001.
    • (2001) Independent Component Analysis
    • Hyvärinen, A.1    Karhunen, J.2    Oja, E.3
  • 17
    • 0028416938 scopus 로고
    • Independent component analysis, a new concept?
    • Comon, P. Independent component analysis, a new concept? Signal Process. 1994, 36, 287-314
    • (1994) Signal Process. , vol.36 , pp. 287-314
    • Comon, P.1
  • 18
    • 84979871553 scopus 로고    scopus 로고
    • Uniqueness of real and complex linear independent component analysis revisited
    • Vienna, Austria
    • Theis, F. Uniqueness of real and complex linear independent component analysis revisited. Proc. European Signal Processing Conference (EUSIPCO); Vienna, Austria, 2004; pp 1705-1708.
    • (2004) Proc. European Signal Processing Conference (EUSIPCO) , pp. 1705-1708
    • Theis, F.1
  • 19
    • 85078284647 scopus 로고    scopus 로고
    • Independent Component Analysis of Electroencephalographic Data
    • In; Touretzky, D. S. Mozer, M. C. Hasselmo, M. E. The MIT Press: Cambridge, MA, Vol
    • Makeig, S.; Bell, A. J.; Jung, T. P.; Sejnowski, T. J. Independent Component Analysis of Electroencephalographic Data. In Advances in Neural Information Processing Systems; Touretzky, D. S.; Mozer, M. C.; Hasselmo, M. E., Eds.; The MIT Press: Cambridge, MA, 1996; Vol. 8, pp 145-151.
    • (1996) Advances in Neural Information Processing Systems , vol.8 , pp. 145-151
    • Makeig, S.1    Bell, A.J.2    Jung, T.P.3    Sejnowski, T.J.4
  • 20
    • 0031861367 scopus 로고    scopus 로고
    • Analysis of fMRI data by blind separation into independent spatial components
    • DOI 10.1002/(SICI)1097-0193(1998)6:3<160::AID-HBM5>3.0.CO;2-1
    • Mckeown, M. J.; Makeig, S.; Brown, G. G.; Jung, T. P.; Kindermann, S. S.; Kindermann, R. S.; Bell, A. J.; Sejnowski, T. J. Analysis of fmri data by blind separation into independent spatial components Hum. Brain Mapping 1998, 6, 160-188 (Pubitemid 28247339)
    • (1998) Human Brain Mapping , vol.6 , Issue.3 , pp. 160-188
    • McKeown, M.J.1    Makeig, S.2    Brown, G.G.3    Jung, T.-P.4    Kindermann, S.S.5    Bell, A.J.6    Sejnowski, T.J.7
  • 23
    • 30744439853 scopus 로고    scopus 로고
    • Molecular diagnosis of human cancer type by gene expression profiles and independent component analysis
    • DOI 10.1038/sj.ejhg.5201495, PII 5201495
    • Zhang, X. W.; Yap, Y. L.; Wei, D.; Chen, F.; Danchin, A. Molecular diagnosis of human cancer type by gene expression profiles and independent component analysis Eur. J. Hum. Genet. 2005, 13 (12) 1303-1311 (Pubitemid 43090533)
    • (2005) European Journal of Human Genetics , vol.13 , Issue.12 , pp. 1303-1311
    • Zhang, X.W.1    Yap, Y.L.2    Wei, D.3    Chen, F.4    Danchin, A.5
  • 24
    • 33747865502 scopus 로고    scopus 로고
    • Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
    • Huang, D. S.; Zheng, C. H. Independent component analysis-based penalized discriminant method for tumor classification using gene expression data Bioinformatics 2006, 22 (15) 1855-1862
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1855-1862
    • Huang, D.S.1    Zheng, C.H.2
  • 25
    • 34548444625 scopus 로고    scopus 로고
    • Elucidating the altered transcriptional programs in breast cancer using independent component analysis
    • Teschendorff, A. E.; Journée, M.; Absil, P. A.; Sepulchre, R.; Caldas, C Elucidating the altered transcriptional programs in breast cancer using independent component analysis PLoS Comput. Biol. 2007, 3 (8) e161
    • (2007) PLoS Comput. Biol. , vol.3 , Issue.8 , pp. 161
    • Teschendorff, A.E.1    Journée, M.2    Absil, P.A.3    Sepulchre, R.4    Caldas, C.5
  • 26
    • 41549100951 scopus 로고    scopus 로고
    • Analyzing m-csf dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis
    • Lutter, D.; Ugocsai, P.; Grandl, M.; Orso, E.; Theis, F.; Lang, E. W.; Schmitz, G. Analyzing m-csf dependent monocyte/macrophage differentiation: expression modes and meta-modes derived from an independent component analysis BMC Bioinformatics 2008, 9, 100
    • (2008) BMC Bioinformatics , vol.9 , pp. 100
    • Lutter, D.1    Ugocsai, P.2    Grandl, M.3    Orso, E.4    Theis, F.5    Lang, E.W.6    Schmitz, G.7
  • 28
    • 77953515457 scopus 로고    scopus 로고
    • Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism
    • Hofmann, J.; Ashry, A. E. N. E.; Anwar, S.; Erban, A.; Kopka, J.; Grundler, F. Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism Plant J. 2010, 62 (6) 1058-1071
    • (2010) Plant J. , vol.62 , Issue.6 , pp. 1058-1071
    • Hofmann, J.1    Ashry, A.E.N.E.2    Anwar, S.3    Erban, A.4    Kopka, J.5    Grundler, F.6
  • 29
    • 65349092907 scopus 로고    scopus 로고
    • Characterization of leaf apoplastic peroxidases and metabolites in vigna unguiculata in response to toxic manganese supply and silicon
    • Führs, H.; Götze, S.; Specht, A.; Erban, A.; Gallien, S.; Heintz, D.; Dorsselaer, A. V.; Kopka, J.; Braun, H. P.; Horst, W. J. Characterization of leaf apoplastic peroxidases and metabolites in vigna unguiculata in response to toxic manganese supply and silicon J. Exp. Bot. 2009, 60 (6) 1663-1678
    • (2009) J. Exp. Bot. , vol.60 , Issue.6 , pp. 1663-1678
    • Führs, H.1    Götze, S.2    Specht, A.3    Erban, A.4    Gallien, S.5    Heintz, D.6    Dorsselaer, A.V.7    Kopka, J.8    Braun, H.P.9    Horst, W.J.10
  • 30
    • 4644240926 scopus 로고    scopus 로고
    • Metabolite fingerprinting: Detecting biological features by independent component analysis
    • DOI 10.1093/bioinformatics/bth270
    • Scholz, M.; Gatzek, S.; Sterling, A.; Fiehn, O.; Selbig, J. Metabolite fingerprinting: Detecting biological features by independent component analysis Bioinformatics 2004, 20 (15) 2447-2454 (Pubitemid 39433366)
    • (2004) Bioinformatics , vol.20 , Issue.15 , pp. 2447-2454
    • Scholz, M.1    Gatzek, S.2    Sterling, A.3    Fiehn, O.4    Selbig, J.5
  • 31
    • 52649132380 scopus 로고    scopus 로고
    • Integration of metabolomic and proteomic phenotypes: Analysis of data covariance dissects starch and rfo metabolism from low and high temperature compensation response in arabidopsis thaliana
    • Wienkoop, S.; Morgenthal, K.; Wolschin, F.; Scholz, M.; Selbig, J.; Weckwerth, W. Integration of metabolomic and proteomic phenotypes: Analysis of data covariance dissects starch and rfo metabolism from low and high temperature compensation response in arabidopsis thaliana Mol. Cell Proteomics 2008, 7 (9) 1725-1736
    • (2008) Mol. Cell Proteomics , vol.7 , Issue.9 , pp. 1725-1736
    • Wienkoop, S.1    Morgenthal, K.2    Wolschin, F.3    Scholz, M.4    Selbig, J.5    Weckwerth, W.6
  • 33
    • 3042594840 scopus 로고    scopus 로고
    • Validating the independent components of neuroimaging time series via clustering and visualization
    • DOI 10.1016/j.neuroimage.2004.03.027, PII S1053811904001661
    • Himberg, J.; Hyvärinen, A.; Esposito, F. Validating the independent components of neuroimaging time series via clustering and visualization NeuroImage 2004, 22 (3) 1214-1222 (Pubitemid 38829210)
    • (2004) NeuroImage , vol.22 , Issue.3 , pp. 1214-1222
    • Himberg, J.1    Hyvarinen, A.2    Esposito, F.3
  • 35
    • 0001387715 scopus 로고    scopus 로고
    • Mean-field approaches to independent component analysis
    • Højen-Sørensen, P. A. R.; Winther, O.; Hansen, L. K. Mean-field approaches to independent component analysis Neural Comput. 2002, 14 (4) 889-918
    • (2002) Neural Comput. , vol.14 , Issue.4 , pp. 889-918
    • Højen-Sørensen, P.A.R.1    Winther, O.2    Hansen, L.K.3
  • 38
    • 0012610855 scopus 로고    scopus 로고
    • Springer-Verlag: London, New York, Chapter: Blind separation of noisy image mixtures
    • Hansen, L. K. Advances in Independent Components Analysis; Springer-Verlag: London, New York, 2000; Chapter: Blind separation of noisy image mixtures, pp 165-187.
    • (2000) Advances in Independent Components Analysis , pp. 165-187
    • Hansen, L.K.1
  • 41
    • 79958115671 scopus 로고    scopus 로고
    • Web-based inference of biological patterns, functions and pathways from metabolomic data using metaboanalyst
    • Xia, J.; Wishart, D. S. Web-based inference of biological patterns, functions and pathways from metabolomic data using metaboanalyst Nat. Protoc. 2011, 6 (6) 743-760
    • (2011) Nat. Protoc. , vol.6 , Issue.6 , pp. 743-760
    • Xia, J.1    Wishart, D.S.2
  • 42
    • 38649110731 scopus 로고    scopus 로고
    • A treasure trove for lipoprotein biology
    • DOI 10.1038/ng0208-129, PII NG0208129
    • Lusis, A. J.; Pajukanta, P. A treasure trove for lipoprotein biology Nat. Genet. 2008, 40 (2) 129-130 (Pubitemid 351171408)
    • (2008) Nature Genetics , vol.40 , Issue.2 , pp. 129-130
    • Lusis, A.J.1    Pajukanta, P.2
  • 43
    • 80054843453 scopus 로고    scopus 로고
    • Weighted correlation network analysis (wgcna) applied to the tomato fruit metabolome
    • DiLeo, M. V.; Strahan, G. D.; den Bakker, M.; Hoekenga, O. A. Weighted correlation network analysis (wgcna) applied to the tomato fruit metabolome PLoS ONE 2011, 6 (10) e26683
    • (2011) PLoS ONE , vol.6 , Issue.10 , pp. 26683
    • Dileo, M.V.1    Strahan, G.D.2    Den Bakker, M.3    Hoekenga, O.A.4
  • 45
    • 80053574090 scopus 로고    scopus 로고
    • Biological activities of hdl subpopulations and their relevance to cardiovascular disease
    • Camont, L.; Chapman, M. J.; Kontush, A. Biological activities of hdl subpopulations and their relevance to cardiovascular disease Trends Mol. Med. 2011, 17 (10) 594-603
    • (2011) Trends Mol. Med. , vol.17 , Issue.10 , pp. 594-603
    • Camont, L.1    Chapman, M.J.2    Kontush, A.3
  • 47
    • 0014669160 scopus 로고
    • Plasma amino acid levels and insulin secretion in obesity
    • Felig, P.; Marliss, E.; Cahill, G. F. Plasma amino acid levels and insulin secretion in obesity N. Engl. J. Med. 1969, 281 (15) 811-816
    • (1969) N. Engl. J. Med. , vol.281 , Issue.15 , pp. 811-816
    • Felig, P.1    Marliss, E.2    Cahill, G.F.3
  • 49
    • 31544440119 scopus 로고    scopus 로고
    • Potential importance of leucine in treatment of obesity and the metabolic syndrome
    • Layman, D. K.; Walker, D. A. Potential importance of leucine in treatment of obesity and the metabolic syndrome J. Nutr. 2006, 136 (1 Suppl.) 319S-323S (Pubitemid 43156532)
    • (2006) Journal of Nutrition , vol.136 , Issue.1
    • Layman, D.K.1    Walker, D.A.2
  • 50
    • 79955466395 scopus 로고    scopus 로고
    • Lipid control in patients with diabetes mellitus
    • Betteridge, D. J. Lipid control in patients with diabetes mellitus Nat. Rev. Cardiol. 2011, 8 (5) 278-290
    • (2011) Nat. Rev. Cardiol. , vol.8 , Issue.5 , pp. 278-290
    • Betteridge, D.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.