Difference between revisions of "James P. McDonald Week 5"

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(KEGG: added last kegg question)
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**GLN1: expression regulated by nitrogen source and amino acid limitation
 
**GLN1: expression regulated by nitrogen source and amino acid limitation
 
**GLT1: expression regulated by nitrogen source
 
**GLT1: expression regulated by nitrogen source
*There are 56 pathways listed in the database that L-glutamate participates
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*There are 56 pathways listed in the database that L-glutamate participates in
*Pathway
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*Pathway:
 
**[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13 SGD Pathway]
 
**[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13 SGD Pathway]
 
**[[image:SGD_Pathway.jpg]]
 
**[[image:SGD_Pathway.jpg]]
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*Parameters:
  
 
===KEGG===
 
===KEGG===
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*[http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=sce00250&keyword=glutamate KEG Pathway]
 
*[http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=sce00250&keyword=glutamate KEG Pathway]
 
*[[image:KEGG_Pathway_edit.jpg]]
 
*[[image:KEGG_Pathway_edit.jpg]]
*
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*This pathway contains a total of 19 enzymes/genes, and there are 12 present in yeast (highlighted).
 
*The information provided in KEGG is similar to SGD but KEGG includes 3-D structures of the enzymes and AA and NT sequences.
 
*The information provided in KEGG is similar to SGD but KEGG includes 3-D structures of the enzymes and AA and NT sequences.
  
 
===Reactome===
 
===Reactome===
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*[http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666285&ID=2659808 Reactome Pathway]
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*[[image:Reactome_Pathway_edit.jpg]]
  
 
{{James P. McDonald}}
 
{{James P. McDonald}}
  
 
[[Category:BIOL398-03/S13]]
 
[[Category:BIOL398-03/S13]]

Revision as of 23:43, 13 February 2013

Exploring Pathway Databases

Saccharomyces Genome Database

  • GDH2 has a homolog in humans. A deficiency of the human homologs, GLUD1 and GLUD2, has been known to cause hyperinsulinism-hyperammonemia syndrome and various neurological disorders.
  • Gene Expression Regulation:
    • 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 amino acid limitation
    • GLT1: expression regulated by nitrogen source
  • There are 56 pathways listed in the database that L-glutamate participates in
  • Pathway:
  • Parameters:

KEGG

  • KEG Pathway
  • KEGG Pathway edit.jpg
  • This pathway contains a total of 19 enzymes/genes, and there are 12 present in yeast (highlighted).
  • The information provided in KEGG is similar to SGD but KEGG includes 3-D structures of the enzymes and AA and NT sequences.

Reactome

Class Links

Journal Entries and Assignments