Individual Journal Week 5

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(Saccharomyces Genome Database: question 3)
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* Find the SGD representation of the pathway we are working on in class and attach a screenshot and hyperlink to your journal page.  Choose the one that shows all of the reactions we talked about in class and make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.
* Find the SGD representation of the pathway we are working on in class and attach a screenshot and hyperlink to your journal page.  Choose the one that shows all of the reactions we talked about in class and make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.
[[Image:Screen Shot 2013-02-14 at 10.04.34 PM.png]]
[[Image:Screen Shot 2013-02-14 at 10.04.34 PM.png]]
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[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13]
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* What parameters for these reactions can you find using this database? ''HINT: the literature portion of the individual gene pages may be helpful.''
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**[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13| SGD Representation]
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* What parameters for these reactions can you find using this database?  
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**Carbon, Nitrogen, and Ammonia feed concentrations tend to be the parameters sited on the database.
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==== KEGG ====
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[[Image:Screen Shot 2013-02-14 at 11.03.54 PM.png]]
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*How many genes in this pathway exist in yeast?
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**There are 19 genes in the pathway. The 12 "green" genes are enzymes that are present in yeast (two have been cut out of screenshot).
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* Is there any new information here that was not represented by SGD?
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**In KEGG, when clicking on the genes, one may view pathways, motifs, and positions, as well as amino acid and nucleotide sequences.
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==== Reactome ====
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[[Image:Screen Shot 2013-02-14 at 11.28.18 PM.png]]
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[[BIOL398-03/S13:Week 5| Week 5 Assignment]]

Current revision

Saccharomyces Genome Database

  • 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 homologue in humans and can result in hyperinsulinism-hyperammonemia syndrome and various neurological disorders as a result of deficiencies.
  • How is the expression of each of these genes regulated?
    • GDH1: expression regulated by nitrogen and carbon sources
    • GDH3: expression regulated by nitrogen and carbon sources
    • GDH2: expression sensitive to nitrogen catabolite repression and intracellular ammonia levels
    • 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?
    • As a product L-glutamate participates in 30 pathways. As a reactant it participates in 26 pathways.
  • Find the SGD representation of the pathway we are working on in class and attach a screenshot and hyperlink to your journal page. Choose the one that shows all of the reactions we talked about in class and make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.

Image:Screen Shot 2013-02-14 at 10.04.34 PM.png

  • What parameters for these reactions can you find using this database?
    • Carbon, Nitrogen, and Ammonia feed concentrations tend to be the parameters sited on the database.

KEGG

Image:Screen Shot 2013-02-14 at 11.03.54 PM.png

  • How many genes in this pathway exist in yeast?
    • There are 19 genes in the pathway. The 12 "green" genes are enzymes that are present in yeast (two have been cut out of screenshot).
  • Is there any new information here that was not represented by SGD?
    • In KEGG, when clicking on the genes, one may view pathways, motifs, and positions, as well as amino acid and nucleotide sequences.

Reactome

Image:Screen Shot 2013-02-14 at 11.28.18 PM.png

Week 5 Assignment

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