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

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(KEGG: answered gene question)
(Saccharomyces Genome Database: added parameters answer)
 
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**[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:
+
*Parameters: The literature contains parameters such as nitrogen feeds, carbon feeds, and conversion rates.
  
 
===KEGG===
 
===KEGG===

Latest revision as of 18:20, 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
  • 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