Elizabeth Polidan Week5
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Elizabeth Polidan
BIOL 398.03 / MATH 388
- Loyola Marymount University
- Los Angeles, CA, USA
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.
- GDH2 has a homolog in humans.
- 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
- L-glutamate participation in pathway reactions
- 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.
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.
- Yes, for example:
Reactome
