Elizabeth Polidan Week5: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(Corrected formatting.) |
(Added link to assignment page) |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
{{Elizabeth_Polidan}} | {{Elizabeth_Polidan}} | ||
[[BIOL398-03/S13:Week_5|Week 5 Assignment]] | |||
'''Saccharomyces Genome Database - SGD''' | '''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? | *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 | ***Deficiencies in the human homologs are linked to hyperinsulinism-hyperammonemia syndrome and neurological disorders. | ||
*How is the expression of each of these genes regulated? | *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 | **GDH1 – expression regulated by Carbon and Nitrogen sources; expression high for both ethanol and glucose | ||
| Line 14: | Line 18: | ||
***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] | ||
[[Image:SGD.jpg]] | [[Image:SGD.jpg]] | ||
---- | ---- | ||
'''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? | |||
**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. | |||
[http://www.genome.jp/kegg-bin/show_pathway?sce00250 KEGG Pathway] | [http://www.genome.jp/kegg-bin/show_pathway?sce00250 KEGG Pathway] | ||
[[Image:KEGG.jpg]] | [[Image:KEGG.jpg]] | ||
---- | ---- | ||
'''Reactome''' | '''Reactome''' | ||
[http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666288&ID=2666287 Reactome] | [http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666288&ID=2666287 Reactome] | ||
[[Image:REACTOME.jpg]] | [[Image:REACTOME.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
