Kasey E. O'Connor Week 5 Journal - Revision history

Kasey E. O'Connor: KEGG and reactome

Kasey E. O'Connor — Fri, 15 Feb 2013 06:29:50 GMT

KEGG and reactome

←Older revision		Revision as of 06:29, 15 February 2013
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	[[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13&detail-level=4&detail-level=3\|Glutamate Biosynthesis Pathway Link]]		[[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13&detail-level=4&detail-level=3\|Glutamate Biosynthesis Pathway Link]]
	#Parameters		#Parameters
		+	The literature found on the SGD site for each enzyme gives informations on the parameters such as carbon concetrations and nitrogen concentrations in feed.

	====KEGG====		====KEGG====
	#Nitrogen Pathway Image		#Nitrogen Pathway Image
		+	[[Image:Capture1.PNG]]
		+	[[http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=sce00250&keyword=glutamate\|KEGG Pathway]]
		+	In this cycle, 12 of the genes are present in yeast cells. These are represented by the green highlighted boxes.
		+
	#New Information?		#New Information?
		+	KEGG gives information on the amino acid and nucleotide sequence on the main page, which is different than SGD. It also provides a 3D image of the enzyme for further structural understanding.

	====Reactome====		====Reactome====
	#Nitrogen Pathway Image		#Nitrogen Pathway Image
-		+	[[Image:Capture3.PNG]]
		+	[[http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=68322&FOCUS_PATHWAY_ID=2666285&ID=2659806&VID=6541308]]

	==Useful Links==		==Useful Links==
	{{Kasey E. O'Connor}}		{{Kasey E. O'Connor}}

Kasey E. O'Connor: SGD

Kasey E. O'Connor — Thu, 14 Feb 2013 05:16:22 GMT

SGD

←Older revision		Revision as of 05:16, 14 February 2013
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	==Exploring Pathway Databases==		==Exploring Pathway Databases==
	====Saccharomyces Genome Database====		====Saccharomyces Genome Database====
-	=====~~=Enzyme Encoding Genes=~~=====	+	http://www.yeastgenome.org
-	#GDH1	+	=====Human Homologues=====
-	#GDH3	+	*GDH1 and GDH3 are homologous to 1NR1 and 1L1F in humans. Deficiency of these genes is linked to hyperinsulinism/hyperammonemia syndrome in humans.
-	#GDH2	+	*GDH2 is homologous to GLUD1 and GLUD2, both of which have a deficiency linked to hyperinsulinism/hyperammonemia syndrome in humans.
-	#GLN1	+	*GLN1 is homologous to 2OJW as well as 2QC8 in humans. A lack of these genes may be linked to neurodegenerative disorders.
-	~~#GLT1~~	+

-	======Pathways and Reactions======	+	=====Enzyme Encoding Genes=====
-	#L-glutamate	+	#GDH1: Expression is regulated by carbon and nitrogen sources, and is high in ethanol and glucose. GDH1 uses alpha-ketogluterate faster than GSH3, so under fermentive conditions, glutamate is synthesized.
		+	#GDH3: Similarly to GDH1, expression is regulated by carbon and nitrogen sources. However, expression is induced by ethanol and repressed by glucose. In situations with limited carbon, GDH3 balances the synthesis of glutamate from alpha-ketogluterate and the energy used for metabolism.
		+	#GDH2: Gene expression is regulated by the concentration of ammonia. As intracellular concentration increases, there is a decrease in expression. But, an increase in extracellular ammonia leads to an increased in the transcription and activity of GDH2.
		+	#GLN1: The expression is regulated by the nitrogen source as well as by amino acid limitation.
		+	#GLT1: Expression depends on the amount of nitrogen and glutamate that is accessible. In conditions with barely any amino acid, GLT1 activation is regulated by GCN4. depending upon the availability of nitrogen and glutamate in the medium. In amino acid starvation conditions, GLT1 expression is activated
		+
		+	=====Pathways and Reactions=====
		+	#L-glutamate is in 56 pathways as a reactant or a product. It is also in 12 reactions that are not assigned to pathways.
	#Nitrogen Pathway Image		#Nitrogen Pathway Image
		+	[[Image:Screen Shot 2013-02-13 at 9.12.58 PM.png\|Glutamate Biosynthesis Pathway]]
		+	[[http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-13&detail-level=4&detail-level=3\|Glutamate Biosynthesis Pathway Link]]
	#Parameters		#Parameters

Kasey E. O'Connor: layout edit

Kasey E. O'Connor — Thu, 14 Feb 2013 04:29:45 GMT

layout edit

←Older revision		Revision as of 04:29, 14 February 2013
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	==Exploring Pathway Databases==		==Exploring Pathway Databases==
		+	====Saccharomyces Genome Database====
		+	======Enzyme Encoding Genes======
		+	#GDH1
		+	#GDH3
		+	#GDH2
		+	#GLN1
		+	#GLT1
		+
		+	======Pathways and Reactions======
		+	#L-glutamate
		+	#Nitrogen Pathway Image
		+	#Parameters
		+
		+	====KEGG====
		+	#Nitrogen Pathway Image
		+	#New Information?
		+
		+	====Reactome====
		+	#Nitrogen Pathway Image
		+

	==Useful Links==		==Useful Links==
	{{Kasey E. O'Connor}}		{{Kasey E. O'Connor}}

Kasey E. O'Connor: add template header

Kasey E. O'Connor — Tue, 12 Feb 2013 17:41:52 GMT

add template header

←Older revision		Revision as of 17:41, 12 February 2013
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	==Exploring Pathway Databases==		==Exploring Pathway Databases==
		+
		+	==Useful Links==
	{{Kasey E. O'Connor}}		{{Kasey E. O'Connor}}

Kasey E. O'Connor: add template

Kasey E. O'Connor — Tue, 12 Feb 2013 17:40:41 GMT

add template

←Older revision		Revision as of 17:40, 12 February 2013
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	==Exploring Pathway Databases==		==Exploring Pathway Databases==
		+	{{Kasey E. O'Connor}}

Kasey E. O'Connor: make page

Kasey E. O'Connor — Tue, 12 Feb 2013 17:39:55 GMT

make page

New page

==Exploring Pathway Databases==