James P. McDonald Week 5: Difference between revisions

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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
*There are 56 pathways listed in the database that L-glutamate participates in
*Pathway
*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]]
*Parameters: The literature contains parameters such as nitrogen feeds, carbon feeds, and conversion rates.


===KEGG===
===KEGG===
Line 18: Line 19:
*[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]]
*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===
===Reactome===
*[http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666285&ID=2659808 Reactome Pathway]
*[[image:Reactome_Pathway_edit.jpg]]


{{James P. McDonald}}
{{James P. McDonald}}


[[Category:BIOL398-03/S13]]
[[Category:BIOL398-03/S13]]

Latest revision as of 19:20, 14 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: The literature contains parameters such as nitrogen feeds, carbon feeds, and conversion rates.

KEGG

  • KEG Pathway
  • 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

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