메뉴 건너뛰기




Volumn 11, Issue 6, 2015, Pages 921-933

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROLIPOAMIDE DEHYDROGENASE; PROTEOME; PYRUVIC ACID; TRANSCRIPTOME; BIOLOGICAL MARKER;

EID: 84929276343     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2015.04.010     Document Type: Article
Times cited : (93)

References (60)
  • 1
    • 77952503211 scopus 로고    scopus 로고
    • Pathogenesis of insulin resistance in skeletal muscle
    • Abdul-Ghani M.A., DeFronzo R.A. Pathogenesis of insulin resistance in skeletal muscle. J.Biomed. Biotechnol. 2010, 2010:476279.
    • (2010) J.Biomed. Biotechnol. , vol.2010 , pp. 476279
    • Abdul-Ghani, M.A.1    DeFronzo, R.A.2
  • 2
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • Agren R., Bordel S., Mardinoglu A., Pornputtapong N., Nookaew I., Nielsen J. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput. Biol. 2012, 8:e1002518.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002518
    • Agren, R.1    Bordel, S.2    Mardinoglu, A.3    Pornputtapong, N.4    Nookaew, I.5    Nielsen, J.6
  • 3
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • Agren R., Liu L., Shoaie S., Vongsangnak W., Nookaew I., Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput. Biol. 2013, 9:e1002980.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1002980
    • Agren, R.1    Liu, L.2    Shoaie, S.3    Vongsangnak, W.4    Nookaew, I.5    Nielsen, J.6
  • 4
    • 84898663879 scopus 로고    scopus 로고
    • Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
    • Agren R., Mardinoglu A., Asplund A., Kampf C., Uhlen M., Nielsen J. Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol. Syst. Biol. 2014, 10:721.
    • (2014) Mol. Syst. Biol. , vol.10 , pp. 721
    • Agren, R.1    Mardinoglu, A.2    Asplund, A.3    Kampf, C.4    Uhlen, M.5    Nielsen, J.6
  • 5
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-a Python framework to work with high-throughput sequencing data
    • Anders S., Pyl P.T., Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31:166-169.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 6
    • 0016723939 scopus 로고
    • Percutaneous needle biopsy of skeletal muscle in physiological and clinical research
    • Bergström J. Percutaneous needle biopsy of skeletal muscle in physiological and clinical research. Scand. J. Clin. Lab. Invest. 1975, 35:609-616.
    • (1975) Scand. J. Clin. Lab. Invest. , vol.35 , pp. 609-616
    • Bergström, J.1
  • 8
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • Bordbar A., Monk J.M., King Z.A., Palsson B.O. Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 2014, 15:107-120.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.O.4
  • 9
    • 33847611885 scopus 로고    scopus 로고
    • Patients with type 2 diabetes have normal mitochondrial function in skeletal muscle
    • Boushel R., Gnaiger E., Schjerling P., Skovbro M., Kraunsøe R., Dela F. Patients with type 2 diabetes have normal mitochondrial function in skeletal muscle. Diabetologia 2007, 50:790-796.
    • (2007) Diabetologia , vol.50 , pp. 790-796
    • Boushel, R.1    Gnaiger, E.2    Schjerling, P.3    Skovbro, M.4    Kraunsøe, R.5    Dela, F.6
  • 11
    • 84858702540 scopus 로고    scopus 로고
    • The worldwide epidemiology of type 2 diabetes mellitus-present and future perspectives
    • Chen L., Magliano D.J., Zimmet P.Z. The worldwide epidemiology of type 2 diabetes mellitus-present and future perspectives. Nat. Rev. Endocrinol. 2012, 8:228-236.
    • (2012) Nat. Rev. Endocrinol. , vol.8 , pp. 228-236
    • Chen, L.1    Magliano, D.J.2    Zimmet, P.Z.3
  • 13
    • 4944232237 scopus 로고    scopus 로고
    • Combining multiple microarray studies and modeling interstudy variation
    • Choi J.K., Yu U., Kim S., Yoo O.J. Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19(Suppl 1):i84-i90.
    • (2003) Bioinformatics , vol.19 , pp. i84-i90
    • Choi, J.K.1    Yu, U.2    Kim, S.3    Yoo, O.J.4
  • 16
    • 79151478555 scopus 로고    scopus 로고
    • Type 2 diabetes as an inflammatory disease
    • Donath M.Y., Shoelson S.E. Type 2 diabetes as an inflammatory disease. Nat. Rev. Immunol. 2011, 11:98-107.
    • (2011) Nat. Rev. Immunol. , vol.11 , pp. 98-107
    • Donath, M.Y.1    Shoelson, S.E.2
  • 17
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 21
    • 80755148685 scopus 로고    scopus 로고
    • Elevated NF-κB activation is conserved in human myocytes cultured from obese type 2 diabetic patients and attenuated by AMP-activated protein kinase
    • Green C.J., Pedersen M., Pedersen B.K., Scheele C. Elevated NF-κB activation is conserved in human myocytes cultured from obese type 2 diabetic patients and attenuated by AMP-activated protein kinase. Diabetes 2011, 60:2810-2819.
    • (2011) Diabetes , vol.60 , pp. 2810-2819
    • Green, C.J.1    Pedersen, M.2    Pedersen, B.K.3    Scheele, C.4
  • 25
    • 18844439409 scopus 로고    scopus 로고
    • Histidine and carnosine delay diabetic deterioration in mice and protect human low density lipoprotein against oxidation and glycation
    • Lee Y.T., Hsu C.C., Lin M.H., Liu K.S., Yin M.C. Histidine and carnosine delay diabetic deterioration in mice and protect human low density lipoprotein against oxidation and glycation. Eur. J. Pharmacol. 2005, 513:145-150.
    • (2005) Eur. J. Pharmacol. , vol.513 , pp. 145-150
    • Lee, Y.T.1    Hsu, C.C.2    Lin, M.H.3    Liu, K.S.4    Yin, M.C.5
  • 26
    • 77957589754 scopus 로고    scopus 로고
    • Increased reactive oxygen species production and lower abundance of complex I subunits and carnitine palmitoyltransferase 1B protein despite normal mitochondrial respiration in insulin-resistant human skeletal muscle
    • Lefort N., Glancy B., Bowen B., Willis W.T., Bailowitz Z., De Filippis E.A., Brophy C., Meyer C., Højlund K., Yi Z., Mandarino L.J. Increased reactive oxygen species production and lower abundance of complex I subunits and carnitine palmitoyltransferase 1B protein despite normal mitochondrial respiration in insulin-resistant human skeletal muscle. Diabetes 2010, 59:2444-2452.
    • (2010) Diabetes , vol.59 , pp. 2444-2452
    • Lefort, N.1    Glancy, B.2    Bowen, B.3    Willis, W.T.4    Bailowitz, Z.5    De Filippis, E.A.6    Brophy, C.7    Meyer, C.8    Højlund, K.9    Yi, Z.10    Mandarino, L.J.11
  • 27
    • 0141929920 scopus 로고    scopus 로고
    • Biomechanics of skeletal muscle
    • Lippincott Williams & Wilkins, Philadelphia, M. Nordin, V.H. Frankel (Eds.)
    • Lorenz T., Campello M. Biomechanics of skeletal muscle. Basic Biomechanics of the Musculoskeletal System 2001, 148-174. Lippincott Williams & Wilkins, Philadelphia. Third Edition. M. Nordin, V.H. Frankel (Eds.).
    • (2001) Basic Biomechanics of the Musculoskeletal System , pp. 148-174
    • Lorenz, T.1    Campello, M.2
  • 29
    • 84927173996 scopus 로고    scopus 로고
    • Branched-chain amino acids in metabolic signalling and insulin resistance
    • Lynch C.J., Adams S.H. Branched-chain amino acids in metabolic signalling and insulin resistance. Nat. Rev. Endocrinol. 2014, 10:723-736.
    • (2014) Nat. Rev. Endocrinol. , vol.10 , pp. 723-736
    • Lynch, C.J.1    Adams, S.H.2
  • 31
    • 84883384697 scopus 로고    scopus 로고
    • Genome-scale modeling of human metabolism - a systems biology approach
    • Mardinoglu A., Gatto F., Nielsen J. Genome-scale modeling of human metabolism - a systems biology approach. Biotechnol. J. 2013, 8:985-996.
    • (2013) Biotechnol. J. , vol.8 , pp. 985-996
    • Mardinoglu, A.1    Gatto, F.2    Nielsen, J.3
  • 32
    • 84898011025 scopus 로고    scopus 로고
    • Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
    • Mardinoglu A., Agren R., Kampf C., Asplund A., Uhlen M., Nielsen J. Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat. Commun. 2014, 5:3083.
    • (2014) Nat. Commun. , vol.5 , pp. 3083
    • Mardinoglu, A.1    Agren, R.2    Kampf, C.3    Asplund, A.4    Uhlen, M.5    Nielsen, J.6
  • 36
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • Patil K.R., Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. USA 2005, 102:2685-2689.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 38
    • 84864283300 scopus 로고    scopus 로고
    • Muscles, exercise and obesity: skeletal muscle as a secretory organ
    • Pedersen B.K., Febbraio M.A. Muscles, exercise and obesity: skeletal muscle as a secretory organ. Nat. Rev. Endocrinol. 2012, 8:457-465.
    • (2012) Nat. Rev. Endocrinol. , vol.8 , pp. 457-465
    • Pedersen, B.K.1    Febbraio, M.A.2
  • 39
    • 84929203519 scopus 로고    scopus 로고
    • Gestational diabetes alters offspring DNA methylation profiles in human and rat: identification of key pathways involved in endocrine system disorders, insulin signaling, diabetes signaling and IL-K signaling
    • Published online December 16, 2014
    • Petropoulos S., Guillemin C., Ergaz Z., Dimov S., Suderman M., Weinstein-Fudim L., Ornoy A., Szyf M. Gestational diabetes alters offspring DNA methylation profiles in human and rat: identification of key pathways involved in endocrine system disorders, insulin signaling, diabetes signaling and IL-K signaling. Endocrinology 2014, Published online December 16, 2014. 10.1210/en.2014-1643.
    • (2014) Endocrinology
    • Petropoulos, S.1    Guillemin, C.2    Ergaz, Z.3    Dimov, S.4    Suderman, M.5    Weinstein-Fudim, L.6    Ornoy, A.7    Szyf, M.8
  • 42
    • 53149135477 scopus 로고    scopus 로고
    • Key issues in conducting a meta-analysis of gene expression microarray datasets
    • Ramasamy A., Mondry A., Holmes C.C., Altman D.G. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med. 2008, 5:e184.
    • (2008) PLoS Med. , vol.5 , pp. e184
    • Ramasamy, A.1    Mondry, A.2    Holmes, C.C.3    Altman, D.G.4
  • 43
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 45
    • 84862729680 scopus 로고    scopus 로고
    • Satellite cells derived from obese humans with type 2 diabetes and differentiated into myocytes invitro exhibit abnormal response to IL-6
    • Scheele C., Nielsen S., Kelly M., Broholm C., Nielsen A.R., Taudorf S., Pedersen M., Fischer C.P., Pedersen B.K. Satellite cells derived from obese humans with type 2 diabetes and differentiated into myocytes invitro exhibit abnormal response to IL-6. PLoS ONE 2012, 7:e39657.
    • (2012) PLoS ONE , vol.7 , pp. e39657
    • Scheele, C.1    Nielsen, S.2    Kelly, M.3    Broholm, C.4    Nielsen, A.R.5    Taudorf, S.6    Pedersen, M.7    Fischer, C.P.8    Pedersen, B.K.9
  • 50
    • 33749239623 scopus 로고    scopus 로고
    • The metabolic syndrome: role of skeletal muscle metabolism
    • Stump C.S., Henriksen E.J., Wei Y., Sowers J.R. The metabolic syndrome: role of skeletal muscle metabolism. Ann. Med. 2006, 38:389-402.
    • (2006) Ann. Med. , vol.38 , pp. 389-402
    • Stump, C.S.1    Henriksen, E.J.2    Wei, Y.3    Sowers, J.R.4
  • 51
    • 84856415487 scopus 로고    scopus 로고
    • The role of mitochondria in insulin resistance and type 2 diabetes mellitus
    • Szendroedi J., Phielix E., Roden M. The role of mitochondria in insulin resistance and type 2 diabetes mellitus. Nat. Rev. Endocrinol. 2012, 8:92-103.
    • (2012) Nat. Rev. Endocrinol. , vol.8 , pp. 92-103
    • Szendroedi, J.1    Phielix, E.2    Roden, M.3
  • 55
    • 84877309040 scopus 로고    scopus 로고
    • Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
    • Väremo L., Nielsen J., Nookaew I. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 2013, 41:4378-4391.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 4378-4391
    • Väremo, L.1    Nielsen, J.2    Nookaew, I.3
  • 56
    • 84883786841 scopus 로고    scopus 로고
    • Novel insights into obesity and diabetes through genome-scale metabolic modeling
    • Väremo L., Nookaew I., Nielsen J. Novel insights into obesity and diabetes through genome-scale metabolic modeling. Front. Physiol. 2013, 4:92.
    • (2013) Front. Physiol. , vol.4 , pp. 92
    • Väremo, L.1    Nookaew, I.2    Nielsen, J.3
  • 57
    • 84923910510 scopus 로고    scopus 로고
    • Kiwi: a tool for integration and visualization of network topology and gene-set analysis
    • Väremo L., Gatto F., Nielsen J. Kiwi: a tool for integration and visualization of network topology and gene-set analysis. BMC Bioinformatics 2014, 15:408.
    • (2014) BMC Bioinformatics , vol.15 , pp. 408
    • Väremo, L.1    Gatto, F.2    Nielsen, J.3
  • 58
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • Vogel C., Marcotte E.M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 2012, 13:227-232.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 59
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • Wang Y., Eddy J.A., Price N.D. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst. Biol. 2012, 6:153.
    • (2012) BMC Syst. Biol. , vol.6 , pp. 153
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.