Dbashour Week 10 - Revision history

Dbashour: added references

2017-12-10T00:14:10Z

added references

Dbashour: /* References */ updated

2017-12-10T00:04:02Z

‎References: updated

Dbashour: added summary

2017-12-09T23:17:09Z

added summary

Dbashour: /* Acknowledgements */

2017-12-09T22:30:36Z

‎Acknowledgements

Dbashour: added deliverables

2017-12-09T22:17:58Z

added deliverables

Dbashour: updated corrections

2017-12-09T22:11:51Z

updated corrections

Show changes

Dbashour: /* Electronic Notebook */ syntax fix

2017-11-07T07:48:49Z

‎Electronic Notebook: syntax fix

Dbashour: added definitions

2017-11-07T07:47:54Z

added definitions

Dbashour: updated electronic notebook

2017-11-06T23:09:09Z

updated electronic notebook

Dbashour: added acknowledgements and references

2017-11-06T23:06:51Z

added acknowledgements and references

@@ Line 77: / Line 77: @@
 #LMU BioDB 2017. (2017). Week 8. Retrieved October 27, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
 #LMU BioDB 2017. (2017). Week 10. Retrieved October 27, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
+#Consortium, G. O. (n.d.). Small molecule metabolic process. Retrieved December 09, 2017, from http://amigo.geneontology.org/amigo/term/GO:0044281

@@ Line 75: / Line 75: @@
 ==References==
-*http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848
+#LMU BioDB 2017. (2017). Week 8. Retrieved October 27, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
-*https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
+#LMU BioDB 2017. (2017). Week 10. Retrieved October 27, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
-*https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8

@@ Line 1: / Line 1: @@
-=='''Homework Assignment'''==
+==Electronic Notebook==
 ==== Clustering and GO Term Enrichment with stem ====
@@ Line 60: / Line 60: @@
 ###*protein modification by small protein conjugation or removal - A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein
 ###**http://amigo.geneontology.org/amigo/term/GO:0070647
-'''The cell reacts to cold shock by changing expression of genes associated with these go terms in order to survive under stressful conditions. When the cell undergoes stress (i.e. cold shock), it undergoes a change of expression of genes that would be effected by this stressful condition. Specifically in this case, we are looking at if GLN3 was deleted, which is a transcription factor, what effects would it have on the cell. Once this is determined, we would be able to decide the function of GLN3 in the cell and its relation to cold shock.
+'''The cell reacts to cold shock by changing expression of genes associated with these go terms in order to survive under stressful conditions. When the cell undergoes stress (i.e. cold shock), it undergoes a change of expression of genes that would be effected by this stressful condition. Specifically in this case, we are looking at if GLN3 was deleted, which is a transcription factor, what effects would it have on the cell. Once this is determined, we would be able to decide the function of GLN3 in yeast and its relation to cold shock.
 ==Deliverable==
 [[Media:DGLN3_ANOVA_DB.xlsx | DGLN3 ANOVA/Stem]] <br>

@@ Line 66: / Line 66: @@
 [[Media:Gene_List_GO_List_DB.zip | DGLN3 Gene List and GO list]] <br>
 ==Acknowledgements==
-*Zack helped me with performing this assignment and analyzing the data. Dr. Dahlquist provided the data through her research on yeast and cold shock. I referred to the [[Week 10]] wiki page to complete this assignment and modified the instructions as well. I also used the deliverable from my [Dbashour_Week_8 |Week 8]] individual assignment to complete this week's assignment.
+*Zack helped me with performing this assignment and analyzing the data. Dr. Dahlquist provided the data through her research on yeast and cold shock. I referred to the [[Week 10]] wiki page to complete this assignment and modified the instructions as well. I also used the deliverable from my [[Dbashour_Week_8 |Week 8]] individual assignment to complete this week's assignment.
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' <br>
 [[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 15:09, 6 November 2017 (PST)
 ==References==
 *http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848
 *https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 *https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8

@@ Line 61: / Line 61: @@
 ###**http://amigo.geneontology.org/amigo/term/GO:0070647
 '''The cell reacts to cold shock by changing expression of genes associated with these go terms in order to survive under stressful conditions. When the cell undergoes stress (i.e. cold shock), it undergoes a change of expression of genes that would be effected by this stressful condition. Specifically in this case, we are looking at if GLN3 was deleted, which is a transcription factor, what effects would it have on the cell. Once this is determined, we would be able to decide the function of GLN3 in the cell and its relation to cold shock.
 ==Acknowledgements==
 *Zack helped me with performing this assignment and analyzing the data. Dr. Dahlquist provided the data through her research on yeast and cold shock. I referred to the [[Week 10]] wiki page to complete this assignment and modified the instructions as well. I also used the deliverable from my [Dbashour_Week_8 |Week 8]] individual assignment to complete this week's assignment.

@@ Line 67: / Line 67: @@
 #There are 4 GO terms are associated with this profile when a corrected p value < 0.05.
 #The 6 terms I chose are...
-#* small molecule metabolic process - The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule <br>
+* small molecule metabolic process - The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule <br>
 http://amigo.geneontology.org/amigo/term/GO:0044281
-#* organic acid catabolic process - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage<br>
+* organic acid catabolic process - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage<br>
 http://amigo.geneontology.org/amigo/term/GO:0016054
-#* hydrolase activity - Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3 <br>
+* hydrolase activity - Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3 <br>
 http://amigo.geneontology.org/amigo/term/GO:0016787
-#* co-enzyme binding - Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed <br>
+* co-enzyme binding - Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed <br>
 http://amigo.geneontology.org/amigo/term/GO:0050662
-#* cellular response to stress - Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation) <br>
+* cellular response to stress - Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation) <br>
 http://amigo.geneontology.org/amigo/term/GO:0033554
-#* protein modification by small protein conjugation or removal - A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein
+* protein modification by small protein conjugation or removal - A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein
 http://amigo.geneontology.org/amigo/term/GO:0070647

← Older revision		Revision as of 23:06, 6 November 2017
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	#* cellular response to stress		#* cellular response to stress
	#* protein modification by small protein conjugation or removal		#* protein modification by small protein conjugation or removal
		+
		+	==Acknowledgements==
		+
		+	==References==