Taur.vil Week 8 - Revision history

Taur.vil: source information and titles I forgot last week

2013-10-25T02:42:57Z

source information and titles I forgot last week

Taur.vil: /* Concluding Paragraph */ typo correction

2013-10-18T07:19:22Z

‎Concluding Paragraph: typo correction

Taur.vil: /* Concluding Paragraph */

2013-10-18T06:35:40Z

‎Concluding Paragraph

Taur.vil: /* Criterion Files */ insert concluding paragraph

2013-10-18T05:49:49Z

‎Criterion Files: insert concluding paragraph

Taur.vil: /* Part 2 */ last comments

2013-10-18T05:49:16Z

‎Part 2: last comments

Taur.vil: /* Tu 10/15/2013 */ Part 2

2013-10-18T05:45:31Z

‎Tu 10/15/2013: Part 2

Taur.vil: /* Th 10/10/2013 */ renamed part 1

2013-10-18T05:38:32Z

‎Th 10/10/2013: renamed part 1

Taur.vil: /* Document Files: */ referential clarity

2013-10-18T05:38:05Z

‎Document Files:: referential clarity

Taur.vil: /* Document Files: */ added 20 go terms & relationships

2013-10-18T05:36:15Z

‎Document Files:: added 20 go terms & relationships

Taur.vil: /* Criterion Files */ why different

2013-10-18T04:36:03Z

‎Criterion Files: why different

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-Uploaded Files:
+[[Week_8| Week 8]] Individual Journal
 ==Question Answers==
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 <!--want z to be high and positive, higher than 2 means p is less than .05

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 The individual GOs were more general than the families. Changes were observed in protein binding (particularly unfolded proteins), endonuclease activity, glucose metabolic process, and aromatic compound biosynthetic process. The only one that was specific was the phosphoenolpyruvate-dependent sugar phosphotransferase system which is another instance of ''Vibrio cholerae'' increasing its uptake of carbohydrates from the environment.
-These different groups of GOs lead to a better idea of how ''Vibrio cholerae'' changes as it becomes infectious. First of all, new transcription factors are expressed that could potential be the driving force for other changes in expression. Second, the import-export balance of the cell adjusts and it's metabolism changes. This can be seen by the changed in symporter activity, transmembrane transporters, and general changes in glucose metabolism. There are also changes in protein folding and structure and changes in the synthesis of aromatic compounds. As a whole, these changes suggest that the infectious state has an accelerated metabolism and a different protein makeup to help it infect the hose organism.
+These different groups of GOs lead to a better idea of how ''Vibrio cholerae'' changes as it becomes infectious. First of all, new transcription factors are expressed that could potential be the driving force for other changes in expression. Second, the import-export balance of the cell adjusts and it's metabolism changes. This can be seen by the changed in symporter activity, transmembrane transporters, and general changes in glucose metabolism. There are also changes in protein folding and structure and changes in the synthesis of aromatic compounds. As a whole, these changes suggest that the infectious state has an accelerated metabolism and a different protein makeup to help it infect the host organism.
 ==Document Files:==

← Older revision		Revision as of 06:35, 18 October 2013
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	===Concluding Paragraph===		===Concluding Paragraph===
		+	Using microarray data, we examined differences in gene expression between a non-infectious, laboratory-grown ''Vibrio cholerae'' and a patient-derived, infective version. In particular, work focused on determining overall differences in gene expression and then focusing on the sixteen gene ontologies(GOs) which showed the most dramatic change in expression between conditions. These sixteen clustered into a two family groups of three ontologies, two groups of two, and six individual gene ontologies. One group of three GOs included sugar transmembrane transporter activity, carbohydrate transmembrane transmitter activity, and protein-N(PI)-phosphohistidine-sugar phosphotransferase activity. Changes in these GOs suggest that one of the major changes in the change from benign to infectious is in the cross-membrane transport of carbohydrates. The other group of three included cation:sugar symporter activity, solute:hydrogen symporter activity, and sugar:hydrogen symporter activity. Like the earlier group of three GOs, these are also groups of genes to bring sugars and ions across cell membranes. Together, these two GO families seem to suggest that the cell is requiring greater amounts of energy while infectious than under laboratory conditions.
		+
		+	One of the two member GO families consisted of cis-trans isomerase activity and its child group of peptidyl-prolyl cis-trans isomerase activity. These two gene families each play a role in modifying protein structures within the cell. The other two member family was concerned with translation regulation and contained a general GO for translation regulator activity and a child group that was specific to nucleic acid binding. This suggests that this family is a TF turned on when ''Vibrio cholerae'' becomes infectious and these transcription factors may be the factor that influences the differential expression in other GOs and drives the cellular change to an infectious pathogen.
		+
		+	The individual GOs were more general than the families. Changes were observed in protein binding (particularly unfolded proteins), endonuclease activity, glucose metabolic process, and aromatic compound biosynthetic process. The only one that was specific was the phosphoenolpyruvate-dependent sugar phosphotransferase system which is another instance of ''Vibrio cholerae'' increasing its uptake of carbohydrates from the environment.
		+
		+	These different groups of GOs lead to a better idea of how ''Vibrio cholerae'' changes as it becomes infectious. First of all, new transcription factors are expressed that could potential be the driving force for other changes in expression. Second, the import-export balance of the cell adjusts and it's metabolism changes. This can be seen by the changed in symporter activity, transmembrane transporters, and general changes in glucose metabolism. There are also changes in protein folding and structure and changes in the synthesis of aromatic compounds. As a whole, these changes suggest that the infectious state has an accelerated metabolism and a different protein makeup to help it infect the hose organism.

	==Document Files:==		==Document Files:==

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 #**The numbers the z-score was based on reflected changes in these earlier values.
 #*These numbers are different because the database was updated between 2009 and 2010 increasing the amount of genes that could match with probes in our dataset and uniprot's system.
 ==Document Files:==

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 #Set a filter on z score (Column N) n for values greater than 2 and another one on PermuteP (Column O) for p<0.05.
 #Had 98  terms left, so filtered number changed (Column I) to values between 5 and 100 and percent changed (Column L) to value greater than 33%. (Limited total results to 16 genes.
+#Searched each GO name in MAPPfinder and looked at nearest relatives for other GOs that appeared on my shortened list. Colored related members the same background color using cell fill (see excel above titled "20 GO Terms and Relationships")

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 # Copied into a new page titled forGenMAPP and inserted column 2 (System Code) where N was entered for each row.
-===Tu 10/15/2013===
+===Part 2===
 #Downloaded GenMAPP, my text files, and the 2009 Vibrio cholerae Gene Database
 #Set the database to the downloaded 2009 Vibrio cholerae Gene Database
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 #*Colored increased as red, decreases as green, and no change as yellow
 #Used GenMAPP tool MAPPFinder to create a table for decreases in gene expression, exported as DecreasedVibrio_2009_TV.
 want z to be high and positive, higher than 2 means p is less than .05
 comparing to zero which is the null hypothesis of no change.
 ) magnitude of change observing
-) variation and number of replicates
+) variation and number of replicates-->

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 ==Digital Notebook:==
-===Th 10/10/2013===
+===Part 1===
 # Downloaded original data (Merrell_Compiled_Raw_Data_Vibrio.xls) from [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae]]
 # Observed that the data collected had already been log transformed (there were negative numbers)

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 :[[Media:Vilgalys_2013_10_10_VibrioFileOne.EX.xls|GO w/ filter]]
 :[[Media:3’-5’-exoribonuclease_activity.mapp|MAPP file]]
-:[[Media:Vilgalys_2013_10_10_VibrioFileOne.gmf|GO mapping file]]
+:[[Media:Vilgalys_2013_10_10_VibrioFileOne.gmf|GO mapping file (.gmf file)]]
 :[[Media:Vilgalys_GO_limited_to_20.xls|20 GO Terms and Relationships]]