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References (56)
-
Qing Yan, W. Sadee (2000)
Human membrane transporter database: A web-accessible relational database for drug transport studies and pharmacogenomicsAAPS PharmSci, 2
-
(2007)
A genome-scale computational study of the interplay between transcriptional regulation and metabolism -
M. Saier, Can Tran, R. Barabote (2005)
TCDB: the Transporter Classification Database for membrane transport protein analyses and informationNucleic Acids Research, 34
-
N. Price, J. Reed, B. Palsson (2004)
Genome-scale models of microbial cells: evaluating the consequences of constraintsNature Reviews Microbiology, 2
-
M. Covert, E. Knight, J. Reed, Markus Herrgård, B. Palsson (2004)
Integrating high-throughput and computational data elucidates bacterial networksNature, 429
-
P. Romero, J. Wagg, Michelle Green, D. Kaiser, Markus Krummenacker, P. Karp (2004)
Computational prediction of human metabolic pathways from the complete human genomeGenome Biology, 6
-
C. Son, S. Bilke, S. Davis, Braden Greer, Jun Wei, C. Whiteford, Qingrong Chen, Nicola Cenacchi, J. Khan (2005)
Database of mRNA gene expression profiles of multiple human organs.Genome research, 15 3
-
MM Domach, SK Leung, RE Cahn, GG Cocks, ML Shuler (2000)
Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A. Reprinted from Biotechnology and Bioengineering 26, 203–216 (1984)Biotechnol. Bioeng., 67
-
M. Cline, M. Smoot, E. Cerami, A. Kuchinsky, Nerius Landys, C. Workman, R. Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, K. Hanspers, Ruth Isserlin, Ryan Kelley, S. Killcoyne, Samad Lotia, Steven Maere, J. Morris, K. Ono, Vuk Pavlovic, A. Pico, A. Vailaya, Peng-Liang Wang, Annette Adler, B. Conklin, L. Hood, Martin Kuiper, C. Sander, Ilya Schmulevich, B. Schwikowski, G. Warner, T. Ideker, Gary Bader (2007)
Integration of biological networks and gene expression data using CytoscapeNature Protocols, 2
-
Yong Zhao, D. Srivastava (2007)
A developmental view of microRNA function.Trends in biochemical sciences, 32 4
-
Schuster S., Klamt S., Weckwerth W., Moldenhauer F., Pfeiffer T. (2002)
Use of network analysis of metabolic systems in bioengineeringBioprocess and Biosystems Engineering, 24
-
Yonatan Bilu, T. Shlomi, N. Barkai, E. Ruppin (2006)
Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic StatesPLoS Computational Biology, 2
-
P. Daran-Lapujade, S. Rossell, W. Gulik, M. Luttik, M. Groot, M. Slijper, A. Heck, J. Daran, J. Winde, H. Westerhoff, J. Pronk, Barbara Bakker (2007)
The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levelsProceedings of the National Academy of Sciences, 104
-
I. Schomburg, Antje Chang, Christian Ebeling, M. Gremse, Christian Heldt, G. Huhn, D. Schomburg (2004)
BRENDA, the enzyme database: updates and major new developmentsNucleic acids research, 32 Database issue
-
P Daran-Lapujade (2004)
Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture studyJ. Biol. Chem., 279
-
Brendan Lanpher, N. Brunetti‐Pierri, Brendan Lee (2006)
Inborn errors of metabolism: the flux from Mendelian to complex diseasesNature Reviews Genetics, 7
-
D. Levine, D. Haynor, J. Castle, S. Stepaniants, M. Pellegrini, M. Mao, Jason Johnson (2006)
Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathwaysGenome Biology, 7
-
R. Mahadevan, C. Schilling (2003)
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.Metabolic engineering, 5 4
-
A. Subramanian, P. Tamayo, V. Mootha, Sayan Mukherjee, B. Ebert, Michael Gillette, A. Paulovich, S. Pomeroy, T. Golub, E. Lander, J. Mesirov (2005)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profilesProceedings of the National Academy of Sciences of the United States of America, 102
-
Thuy Vo, H. Greenberg, B. Palsson (2004)
Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data*Journal of Biological Chemistry, 279
-
T. Shlomi, O. Berkman, E. Ruppin (2005)
Regulatory on/off minimization of metabolic flux changes after genetic perturbations.Proceedings of the National Academy of Sciences of the United States of America, 102 21
-
O. Shmueli, S. Horn-Saban, V. Chalifa-Caspi, M. Shmoish, R. Ophir, H. Benjamin-Rodrig, M. Safran, E. Domany, D. Lancet (2003)
GeneNote: whole genome expression profiles in normal human tissues.Comptes rendus biologies, 326 10-11
-
V. McKusick (2007)
Mendelian Inheritance in Man and Its Online Version, OMIMAmerican Journal of Human Genetics, 80
-
Homin Lee, William Braynen, K. Keshav, P. Pavlidis (2005)
ErmineJ: Tool for functional analysis of gene expression data setsBMC Bioinformatics, 6
-
A. Su, T. Wiltshire, S. Batalov, H. Lapp, K. Ching, David Block, Jie Zhang, R. Soden, M. Hayakawa, Gabriel Kreiman, M. Cooke, J. Walker, J. Hogenesch (2004)
A gene atlas of the mouse and human protein-encoding transcriptomes.Proceedings of the National Academy of Sciences of the United States of America, 101 16
-
J. Andersen, Y. Lam, A. Leung, Shao-En Ong, C. Lyon, A. Lamond, M. Mann (2005)
Nucleolar proteome dynamicsNature, 433
-
Iman Famili, Jochen Förster, J. Nielsen, B. Palsson (2003)
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic networkProceedings of the National Academy of Sciences of the United States of America, 100
-
A. Chatziioannou, G. Palaiologos, F. Kolisis (2003)
Metabolic flux analysis as a tool for the elucidation of the metabolism of neurotransmitter glutamate.Metabolic engineering, 5 3
-
(2007)
Nucleic Acids Res -
P. Daran-Lapujade, M. Jansen, J. Daran, W. Gulik, J. Winde, J. Pronk (2004)
Role of Transcriptional Regulation in Controlling Fluxes in Central Carbon Metabolism of Saccharomyces cerevisiaeJournal of Biological Chemistry, 279
-
Goparani Mishra, M. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K. Shivakumar, N. Anuradha, R. Reddy, T. Raghavan, Shalini Menon, G. Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M. Mahesh, Bincy Jacob, Pinky Mathew, P. Chatterjee, K. Arun, Salil Sharma, K. Chandrika, Nandan Deshpande, Kshitish Palvankar, R. Raghavnath, R. Krishnakanth, H. Karathia, B. Rekha, R. Nayak, G. Vishnupriya, H. Kumar, M. Nagini, Sameer Kumar, Rojan Jose, P. Deepthi, S. Mohan, T. Gandhi, H. Harsha, K. Deshpande, M. Sarker, T. Prasad, A. Pandey
Human Protein Reference Database—2009 Update -
Harry Greene, B. Brown, D. McClenathan, R. Agostini, Suzanne Taylor (1988)
A new variant of type IV glycogenosis: Deficiency of branching enzyme activity without apparent progressive liver diseaseHepatology, 8
-
A. Burgard, Prit Pharkya, C. Maranas (2003)
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimizationBiotechnology and Bioengineering, 84
-
D. Kell (2007)
Metabolomic biomarkers: search, discovery and validationExpert Review of Molecular Diagnostics, 7
-
I. Yanai, H. Benjamin-Rodrig, M. Shmoish, V. Chalifa-Caspi, M. Shklar, R. Ophir, A. Bar‐Even, S. Horn-Saban, M. Safran, E. Domany, D. Lancet, O. Shmueli (2005)
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specificationBioinformatics, 21 5
-
D. Wishart, D. Tzur, Craig Knox, Roman Eisner, Anchi Guo, N. Young, D. Cheng, K. Jewell, David Arndt, S. Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, M. Coutouly, I. Forsythe, Peter Tang, S. Shrivastava, Kevin Jeroncic, P. Stothard, G. Amegbey, David Block, D. Hau, James Wagner, Jessica Miniaci, M. Clements, M. Gebremedhin, Natalie Guo, Y. Zhang, G. Duggan, Glen MacInnis, Alim Weljie, R. Dowlatabadi, F. Bamforth, D. Clive, R. Greiner, Liang Li, T. Marrie, B. Sykes, H. Vogel, Lori Querengesser (2007)
HMDB: the Human Metabolome DatabaseNucleic Acids Research, 35
-
S. Rossell, C. Weijden, A. Lindenbergh, A. Tuijl, C. Francke, Barbara Bakker, H. Westerhoff (2006)
Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiaeProceedings of the National Academy of Sciences of the United States of America, 103
-
S. Fong, B. Palsson (2004)
Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypesNature Genetics, 36
-
N. Price, J. Papin, C. Schilling, B. Palsson (2003)
Genome-scale microbial in silico models: the constraints-based approach.Trends in biotechnology, 21 4
-
(2007)
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli -
H. Ogata, S. Goto, Kazushige Sato, W. Fujibuchi, H. Bono, M. Kanehisa (1999)
KEGG: Kyoto Encyclopedia of Genes and GenomesNucleic acids research, 27 1
-
Yuguang Shi, P. Burn (2004)
Lipid metabolic enzymes: emerging drug targets for the treatment of obesityNature Reviews Drug Discovery, 3
-
D. Fell (1996)
Understanding the Control of Metabolism -
Natalie Duarte, S. Becker, N. Jamshidi, I. Thiele, Monica Mo, Thuy Vo, R. Srivas, B. Palsson (2007)
Global reconstruction of the human metabolic network based on genomic and bibliomic dataProceedings of the National Academy of Sciences, 104
-
R. Shyamsundar, Young Kim, J. Higgins, K. Montgomery, M. Jorden, A. Sethuraman, M. Rijn, D. Botstein, P. Brown, J. Pollack (2005)
A DNA microarray survey of gene expression in normal human tissuesGenome Biology, 6
-
D. Muoio, C. Newgard (2006)
Obesity-related derangements in metabolic regulation.Annual review of biochemistry, 75
-
M. Domach, S. Leung, R. Cahn, G. Cocks, M. Shuler (1984)
Computer model for glucose‐limited growth of a single cell of Escherichia coli B/r‐ABiotechnology and Bioengineering, 26
-
J. Brosnan, M. Brosnan (2006)
Branched-chain amino acids: enzyme and substrate regulation.The Journal of nutrition, 136 1 Suppl
-
S. Tay, H. Akman, W. Chung, M. Pike, F. Muntoni, A. Hays, S. Shanske, S. Valberg, J. Mickelson, K. Tanji, S. Dimauro (2004)
Fatal infantile neuromuscular presentation of glycogen storage disease type IVNeuromuscular Disorders, 14
-
M. Åkesson, Jochen Förster, J. Nielsen (2004)
Integration of gene expression data into genome-scale metabolic models.Metabolic engineering, 6 4
-
E. Winter, L. Goodstadt, C. Ponting (2003)
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes.Genome research, 14 1
-
Sharon Wiback, B. Palsson (2002)
Extreme pathway analysis of human red blood cell metabolism.Biophysical journal, 83 2
-
M. Böhm, K. Rosée, R. Schwinger, E. Erdmann (1995)
Evidence for reduction of norepinephrine uptake sites in the failing human heart.Journal of the American College of Cardiology, 25 1
-
L. Altucci, M. Leibowitz, K. Ogilvie, A. Lera, H. Gronemeyer (2007)
RAR and RXR modulation in cancer and metabolic diseaseNature Reviews Drug Discovery, 6
-
Hongwu Ma, A. Sorokin, A. Mazein, A. Selkov, E. Selkov, O. Demin, I. Goryanin (2007)
The Edinburgh human metabolic network reconstruction and its functional analysisMolecular Systems Biology, 3
-
T. Hubbard, Bronwen Aken, Kathryn Beal, B. Ballester, M. Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, T. Cutts, T. Down, S. Dyer, Stephen Fitzgerald, J. Fernandez-Banet, S. Gräf, Syed Haider, M. Hammond, Javier Herrero, Richard Holland, K. Howe, K. Howe, Nathan Johnson, Andreas Kähäri, Damian Keefe, F. Kokocinski, Eugene Kulesha, D. Lawson, Ian Longden, Craig Melsopp, K. Megy, P. Meidl, B. Overduin, Anne Parker, A. Prlić, S. Rice, Daniel Rios, Michael Schuster, I. Sealy, J. Severin, G. Slater, D. Smedley, Giulietta Spudich, S. Trevanion, Albert Vilella, J. Vogel, S. White, M. Wood, Tony Cox, V. Curwen, R. Durbin, X. Fernández-Suárez, P. Flicek, A. Kasprzyk, G. Proctor, S. Searle, James Smith, A. Ureta-Vidal, E. Birney (2006)
Ensembl 2007Nucleic Acids Research, 35
- Publisher
- Springer Journals
- Copyright
- Copyright © 2008 by Nature Publishing Group
- Subject
- Life Sciences; Life Sciences, general; Biotechnology; Biomedicine, general; Agriculture; Biomedical Engineering/Biotechnology; Bioinformatics
- ISSN
- 1087-0156
- eISSN
- 1546-1696
- DOI
- 10.1038/nbt.1487
- Publisher site
- See Article on Publisher Site
Abstract
Metabolic network modeling in multicellular organisms is confounded by the existence of multiple tissues with distinct metabolic functions. By integrating a genome-scale metabolic network with tissue-specific gene- and protein-expression data, Shlomi et al. adapt constraint-based approaches used for microorganisms to predicting metabolism in ten human tissues. Their computational approach should facilitate interpretation of expression data in the context of metabolic disorders.
Journal
Nature Biotechnology – Springer Journals
Published: Aug 17, 2008