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The Metabolic Atlas

The Metabolic Atlas portion of the Tissue Atlas enables exploration of protein function and tissue-specific gene expression in the context of the human metabolic network. For proteins involved in metabolism, a metabolic summary is provided that describes the metabolic subsystems/pathways, cellular compartments, and number of reactions associated with each protein. Over 120 manually curated metabolic pathway maps facilitate the visualization of each protein’s participation in different metabolic processes.

Key publication

Other selected publications

  • Mardinoglu A et al., Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol Syst Biol. (2013)
    PubMed: 23511207 DOI: 10.1038/msb.2013.5

  • Gatto F et al., Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma. Proc Natl Acad Sci U S A. (2014)
    PubMed: 24550497 DOI: 10.1073/pnas.1319196111

  • Mardinoglu A et al., Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat Commun. (2014)
    PubMed: 24419221 DOI: 10.1038/ncomms4083

  • Agren R et al., Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol Syst Biol. (2014)
    PubMed: 24646661 

Figure legend: The Metabolic Atlas provides an overview of all metabolic reactions operating in the human cell (yeast is also available, and other cell types will be added in the future). In addition to being a repository of data, the atlas provides a visualization of metabolism, including links between metabolites, proteins, and genes.

Key facts

  • The Human Metabolic Atlas encompass 13,417 reactions linking 4,164 unique metabolites and 3,625 genes
  • The atlas provides genome-scale metabolic models for 53 healthy tissues and 33 cancers
  • The genome-scale metabolic model for human cells, Human1, can be used to predict gene essentiality in many human cell lines
  • The Human1 model has been expanded to include kinetic information enabling enzyme-constrained model simulations