Difference between revisions of "Lena Week 8"

Revision as of 19:01, 15 October 2013

I used the 2009 version of the Vibrio cholerae Gene Database with GenMAPP.
I loaded my txt file of Vibrio cholerae, and allowed Expression Dataset Manager to convert the data.
The processed data was saved here. Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.gex
The exception file was saved here. Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.EX.txt
There were 772 errors due to genes not being found.
I had more errors than my partner who was using the updated version, she has 122. I think the updated version probably had a more comprehensive list of genes for Vibrio cholerae.

I customized the data set of Avg_LogFC_all with colors. Increased was set to pink and decreased was set to green. To create the criterion for increased I set the Fold Change to > 0.25 and the P Value to < 0.05. To set the criterion for decreased I set Fold Change to < -0.25 and P Value to < 0.05.

My Partner and I worked on the increased criterion.
From GenMAPP I launched MAPPFinder and opened the expression data set file listed above. I clicked on the "Increased" citeria, and checked boxes for "Gene Ontology" and "P Value." In the Browse box, I named the file Increased_LH_20131015-Criterion0-GO.
I ran the MAPPFinder. The top 10 Gene Ontology terms were...

I clicked on the GO term nucleotidyltransferase activity and this window came up. There were significant decreases in three places for VC0647.

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 *COMPARE WITH BUDDY!!!!!
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-* I clicked on the GO term nucleotidyltransferase activity and this window came up.  [[Image:Capture8.PNG]]
+* I clicked on the GO term nucleotidyltransferase activity and this window came up.  There were significant decreases in  three places for VC0647.  [[Image:Capture8.PNG]]
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