메뉴 건너뛰기




Volumn 12, Issue 4, 2016, Pages

Transcriptomics resources of human tissues and organs

Author keywords

genome scale metabolic models; proteomics; transcriptomics

Indexed keywords

RNA; TRANSCRIPTOME;

EID: 84964506792     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20155865     Document Type: Review
Times cited : (109)

References (83)
  • 1
    • 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, (2012) Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 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
  • 2
    • 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, (2014) Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol Syst Biol 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
  • 3
    • 0030895921 scopus 로고    scopus 로고
    • A comparison of selected mRNA and protein abundances in human liver
    • Anderson L, Seilhamer J, (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18: 533-537
    • (1997) Electrophoresis , vol.18 , pp. 533-537
    • Anderson, L.1    Seilhamer, J.2
  • 4
    • 84930989441 scopus 로고    scopus 로고
    • Human genetics: GTEx pilot quantifies eQTL variation across tissues and individuals
    • Bahcall OG, (2015) Human genetics: GTEx pilot quantifies eQTL variation across tissues and individuals. Nat Rev Genet 16: 375
    • (2015) Nat Rev Genet , vol.16 , pp. 375
    • Bahcall, O.G.1
  • 6
    • 84962649780 scopus 로고    scopus 로고
    • Personalized Cardiovascular Disease Prediction and Treatment-A Review of Existing Strategies and Novel Systems Medicine Tools
    • Bjornson E, Boren J, Mardinoglu A, (2016) Personalized Cardiovascular Disease Prediction and Treatment-A Review of Existing Strategies and Novel Systems Medicine Tools. Front Physiol 7: 2
    • (2016) Front Physiol , vol.7 , pp. 2
    • Bjornson, E.1    Boren, J.2    Mardinoglu, A.3
  • 8
    • 77958537509 scopus 로고    scopus 로고
    • Insight into human alveolar macrophage and M. Tuberculosis interactions via metabolic reconstructions
    • Bordbar A, Lewis NE, Schellenberger J, Palsson BO, Jamshidi N, (2010) Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol 6: 422
    • (2010) Mol Syst Biol , vol.6 , pp. 422
    • Bordbar, A.1    Lewis, N.E.2    Schellenberger, J.3    Palsson, B.O.4    Jamshidi, N.5
  • 10
    • 79960169210 scopus 로고    scopus 로고
    • IAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states
    • Bordbar A, Jamshidi N, Palsson BO, (2011b) iAB-RBC-283: a proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Syst Biol 5: 110
    • (2011) BMC Syst Biol , vol.5 , pp. 110
    • Bordbar, A.1    Jamshidi, N.2    Palsson, B.O.3
  • 11
    • 64349094767 scopus 로고    scopus 로고
    • Tissue specificity and the human protein interaction network
    • Bossi A, Lehner B, (2009) Tissue specificity and the human protein interaction network. Mol Syst Biol 5: 260
    • (2009) Mol Syst Biol , vol.5 , pp. 260
    • Bossi, A.1    Lehner, B.2
  • 13
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • Chang RL, Xie L, Bourne PE, Palsson BO, (2010) Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol 6: e1000938
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000938
    • Chang, R.L.1    Xie, L.2    Bourne, P.E.3    Palsson, B.O.4
  • 14
    • 84929001104 scopus 로고    scopus 로고
    • Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
    • GTEx Consortium
    • GTEx Consortium (2015) Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348: 648-660
    • (2015) Science , vol.348 , pp. 648-660
  • 16
    • 84941241201 scopus 로고    scopus 로고
    • Assessing the consistency of public human tissue RNA-seq data sets
    • Danielsson F, James T, Gomez-Cabrero D, Huss M, (2015) Assessing the consistency of public human tissue RNA-seq data sets. Brief Bioinform 16: 941-949
    • (2015) Brief Bioinform , vol.16 , pp. 941-949
    • Danielsson, F.1    James, T.2    Gomez-Cabrero, D.3    Huss, M.4
  • 21
  • 23
    • 84895833353 scopus 로고    scopus 로고
    • Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma
    • Gatto F, Nookaew I, Nielsen J, (2014) Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma. Proc Natl Acad Sci USA 111: E866-E875
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. E866-E875
    • Gatto, F.1    Nookaew, I.2    Nielsen, J.3
  • 24
    • 84930662704 scopus 로고    scopus 로고
    • Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism
    • Gatto F, Miess H, Schulze A, Nielsen J, (2015) Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Sci Rep 5: 10738
    • (2015) Sci Rep , vol.5 , pp. 10738
    • Gatto, F.1    Miess, H.2    Schulze, A.3    Nielsen, J.4
  • 25
    • 84936890106 scopus 로고    scopus 로고
    • Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
    • Ghaffari P, Mardinoglu A, Asplund A, Shoaie S, Kampf C, Uhlen M, Nielsen J, (2015) Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. Sci Rep 5: 8183
    • (2015) Sci Rep , vol.5 , pp. 8183
    • Ghaffari, P.1    Mardinoglu, A.2    Asplund, A.3    Shoaie, S.4    Kampf, C.5    Uhlen, M.6    Nielsen, J.7
  • 26
    • 84929223174 scopus 로고    scopus 로고
    • Human genetics. GTEx detects genetic effects
    • Gibson G, (2015) Human genetics. GTEx detects genetic effects. Science 348: 640-641
    • (2015) Science , vol.348 , pp. 640-641
    • Gibson, G.1
  • 33
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
    • Jerby L, Shlomi T, Ruppin E, (2010) Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 6: 401
    • (2010) Mol Syst Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 36
    • 84941268169 scopus 로고    scopus 로고
    • The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine
    • Keen JC, Moore HM, (2015) The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine. J Pers Med 5: 22-29
    • (2015) J Pers Med , vol.5 , pp. 22-29
    • Keen, J.C.1    Moore, H.M.2
  • 38
    • 84859740873 scopus 로고    scopus 로고
    • RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing
    • Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A, (2012) RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics 28: 1184-1185
    • (2012) Bioinformatics , vol.28 , pp. 1184-1185
    • Krupp, M.1    Marquardt, J.U.2    Sahin, U.3    Galle, P.R.4    Castle, J.5    Teufel, A.6
  • 43
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado D, Herrgard M, (2014) Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol 10: e1003580
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003580
    • MacHado, D.1    Herrgard, M.2
  • 44
    • 71149108056 scopus 로고    scopus 로고
    • Correlation of mRNA and protein in complex biological samples
    • Maier T, Guell M, Serrano L, (2009) Correlation of mRNA and protein in complex biological samples. FEBS Lett 583: 3966-3973
    • (2009) FEBS Lett , vol.583 , pp. 3966-3973
    • Maier, T.1    Guell, M.2    Serrano, L.3
  • 46
    • 84855955467 scopus 로고    scopus 로고
    • Systems medicine and metabolic modelling
    • Mardinoglu A, Nielsen J, (2012) Systems medicine and metabolic modelling. J Intern Med 271: 142-154
    • (2012) J Intern Med , vol.271 , pp. 142-154
    • Mardinoglu, A.1    Nielsen, J.2
  • 48
    • 84883384697 scopus 로고    scopus 로고
    • Genome-scale modeling of human metabolism - A systems biology approach
    • Mardinoglu A, Gatto F, Nielsen J, (2013b) Genome-scale modeling of human metabolism-a systems biology approach. Biotechnol J 8: 985-996
    • (2013) Biotechnol J , vol.8 , pp. 985-996
    • Mardinoglu, A.1    Gatto, F.2    Nielsen, J.3
  • 49
    • 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, (2014a) Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat Commun 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
  • 51
    • 84920286423 scopus 로고    scopus 로고
    • New paradigms for metabolic modeling of human cells
    • Mardinoglu A, Nielsen J, (2015) New paradigms for metabolic modeling of human cells. Curr Opin Biotech 34: 91-97
    • (2015) Curr Opin Biotech , vol.34 , pp. 91-97
    • Mardinoglu, A.1    Nielsen, J.2
  • 54
    • 84940550197 scopus 로고    scopus 로고
    • Mapping proteins with spatial proteomics
    • Marx V, (2015) Mapping proteins with spatial proteomics. Nat Methods 12: 815-819
    • (2015) Nat Methods , vol.12 , pp. 815-819
    • Marx, V.1
  • 57
    • 84930227327 scopus 로고    scopus 로고
    • Using Genome-scale Models to Predict Biological Capabilities
    • O'Brien EJ, Monk JM, Palsson BO, (2015) Using Genome-scale Models to Predict Biological Capabilities. Cell 161: 971-987
    • (2015) Cell , vol.161 , pp. 971-987
    • O'Brien, E.J.1    Monk, J.M.2    Palsson, B.O.3
  • 58
    • 13444278821 scopus 로고    scopus 로고
    • Reconstruction of cellular signalling networks and analysis of their properties
    • Papin JA, Hunter T, Palsson BO, Subramaniam S, (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6: 99-111
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 99-111
    • Papin, J.A.1    Hunter, T.2    Palsson, B.O.3    Subramaniam, S.4
  • 60
    • 20444500207 scopus 로고    scopus 로고
    • Identification of regulatory targets of tissue-specific transcription factors: Application to retina-specific gene regulation
    • Qian J, Esumi N, Chen Y, Wang Q, Chowers I, Zack DJ, (2005) Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. Nucleic Acids Res 33: 3479-3491
    • (2005) Nucleic Acids Res , vol.33 , pp. 3479-3491
    • Qian, J.1    Esumi, N.2    Chen, Y.3    Wang, Q.4    Chowers, I.5    Zack, D.J.6
  • 68
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: A hub for protein information
    • UniProt C, (2015) UniProt: a hub for protein information. Nucleic Acids Res 43: D204-D212
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
    • UniProt, C.1
  • 69
    • 84929276343 scopus 로고    scopus 로고
    • Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes
    • Varemo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlen M, Pedersen BK, Nielsen J, (2015) Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes. Cell Rep 11: 921-933
    • (2015) Cell Rep , vol.11 , pp. 921-933
    • Varemo, L.1    Scheele, C.2    Broholm, C.3    Mardinoglu, A.4    Kampf, C.5    Asplund, A.6    Nookaew, I.7    Uhlen, M.8    Pedersen, B.K.9    Nielsen, J.10
  • 70
    • 84896701551 scopus 로고    scopus 로고
    • Fast reconstruction of compact context-specific metabolic network models
    • Vlassis N, Pacheco MP, Sauter T, (2014) Fast reconstruction of compact context-specific metabolic network models. PLoS Comput Biol 10: e1003424
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003424
    • Vlassis, N.1    Pacheco, M.P.2    Sauter, T.3
  • 71
    • 4544288672 scopus 로고    scopus 로고
    • Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data
    • Vo TD, Greenberg HJ, Palsson BO, (2004) Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem 279: 39532-39540
    • (2004) J Biol Chem , vol.279 , pp. 39532-39540
    • Vo, T.D.1    Greenberg, H.J.2    Palsson, B.O.3
  • 72
    • 34047264333 scopus 로고    scopus 로고
    • Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome
    • Vo TD, Paul Lee WN, Palsson BO, (2007) Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. Mol Genet Metab 91: 15-22
    • (2007) Mol Genet Metab , vol.91 , pp. 15-22
    • Vo, T.D.1    Paul Lee, W.N.2    Palsson, B.O.3
  • 74
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • Wang YL, Eddy JA, Price ND, (2012) Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol 6: 153
    • (2012) BMC Syst Biol , vol.6 , pp. 153
    • Wang, Y.L.1    Eddy, J.A.2    Price, N.D.3
  • 75
    • 0035997009 scopus 로고    scopus 로고
    • Extreme pathway analysis of human red blood cell metabolism
    • Wiback SJ, Palsson BO, (2002) Extreme pathway analysis of human red blood cell metabolism. Biophys J 83: 808-818
    • (2002) Biophys J , vol.83 , pp. 808-818
    • Wiback, S.J.1    Palsson, B.O.2
  • 78
    • 84886670153 scopus 로고    scopus 로고
    • Model-based identification of drug targets that revert disrupted metabolism and its application to ageing
    • Yizhak K, Gabay O, Cohen H, Ruppin E, (2013) Model-based identification of drug targets that revert disrupted metabolism and its application to ageing. Nat Commun 4: 2632
    • (2013) Nat Commun , vol.4 , pp. 2632
    • Yizhak, K.1    Gabay, O.2    Cohen, H.3    Ruppin, E.4
  • 83
    • 84941656865 scopus 로고    scopus 로고
    • Logical transformation of genome-scale metabolic models for gene level applications and analysis
    • Zhang C, Ji B, Mardinoglu A, Nielsen J, Hua Q, (2015) Logical transformation of genome-scale metabolic models for gene level applications and analysis. Bioinformatics 31: 2324-2331
    • (2015) Bioinformatics , vol.31 , pp. 2324-2331
    • Zhang, C.1    Ji, B.2    Mardinoglu, A.3    Nielsen, J.4    Hua, Q.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.