Elizabeth Polidan Week5: Difference between revisions
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[[BIOL398-03/S13:Week_5|Week 5 Assignment]] | |||
'''Saccharomyces Genome Database - SGD''' | '''Saccharomyces Genome Database - SGD''' | ||
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***As a reactant: 26 | ***As a reactant: 26 | ||
***As a product: 30 | ***As a product: 30 | ||
* | *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. | |||
[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] | ||
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[[Image:SGD.jpg]] | [[Image:SGD.jpg]] | ||
---- | ---- | ||
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'''Kyoto Encyclopedia of Genes and Genomes - KEGG''' | '''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? | *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 | **12 | ||
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***Sequences are right up front, not just links. | ***Sequences are right up front, not just links. | ||
***A lot of it is just presented in different ways. | ***A lot of it is just presented in different ways. | ||
[http://www.genome.jp/kegg-bin/show_pathway?sce00250 KEGG Pathway] | |||
[[Image:KEGG.jpg]] | |||
Latest revision as of 22:06, 25 April 2013
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
