Elizabeth Polidan Week5

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Elizabeth Polidan

BIOL 398.03 / MATH 388

  • Loyola Marymount University
  • Los Angeles, CA, USA

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Saccharomyces Genome Database - SGD

  • Which of these genes has a homolog (similar gene related by descent) in humans? What disease does a deficiency of this gene cause in humans?
    • GDH2 has a homolog in humans.
      • Deficiencies in the human homologs are linked to hyperinsulinism-hyperammonemia syndrome and neurological disorders.
  • How is the expression of each of these genes regulated?
    • GDH1 – expression regulated by Carbon and Nitrogen sources; expression high for both ethanol and glucose
    • GDH3 – expression regulated by Carbon and Nitrogen sources; induced by ethanol and repressed by glucose
    • GDH2 – expression regulated by ammonia concentration
    • GLN1 – expression regulated by nitrogen source and by amino acid limitation
    • GLT1 – expression regulated by nitrogen source
  • Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
    • L-glutamate participation in pathway reactions
      • As a reactant: 26
      • As a product: 30
  • What parameters for these reactions can you find using this database? HINT: the literature portion of the individual gene pages may be helpful.
    • The extensive references for these genes will provide concentrations, feed rates, limiting rates, and experimental data from which we can extract parameters.

SGD Pathway

Image:SGD.jpg



Kyoto Encyclopedia of Genes and Genomes - KEGG

  • KEGG also uses a system where a "master" summary pathway compiled from many different organisms is then highlighted with the organism-specific enzymes/genes. How many genes in this pathway exist in yeast?
    • 12
  • Click on each of the five enzymes of our pathway and read the individual enzyme pages. Is there any new information here that was not represented by SGD?
    • Yes, for example:
      • Reference strings for other databases, not just links.
      • Sequences are right up front, not just links.
      • A lot of it is just presented in different ways.

KEGG Pathway

Image:KEGG.jpg



Reactome

Reactome

Image:REACTOME.jpg

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