Difference between revisions of "Lena Week 8"
From LMU BioDB 2013
(→Microarray Data Analysis) |
|||
| Line 60: | Line 60: | ||
| − | ==Microarray Data Analysis== | + | =='''Microarray Data Analysis'''== |
Revision as of 16:31, 17 October 2013
Contents |
Part 1
- Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20131015.txt
- Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20131015.xls
Part 2
GenMAPP Expression Dataset Manager Procedure
- 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.
- The .gex file was saved here. Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.gex
MAPPFinder Procedure
- 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...
- Transport Activity
- Localization
- Macromolecule Metabolic Process
- Cellular Macromolecule Metabolic Process
- Cellular Bipolymer Biosnythetic Process
- Bipolymer Biosnythetic Process
- Bipolymer Metabolic Process
- Amino Acid Metabloic Process
- Cellular Amino Acid and Derivative Metabolic Process
- Cellular Nitrogen Compound Metabolic Process
- Here is an image of the results.
- COMPARE LIST WITH BUDDY!!!!!!!!
- I searched GO terms associated with the genes mentioned by Merrel et al.
- VC0028
- VC0941
- VC0869
- VC0051
- VC0647
- VC2350
- VCA0583
- COMPARE WITH BUDDY!!!!!
- I clicked on the GO term nucleotidyltransferase activity and this window came up. There were significant decreases in three places for VC0647.
Uploaded Files
- Exception Files: Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.EX.txt
- Expression Dataset file: Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.gex
- GO Results file: Media:Increased_LH_20131015-Criterion0-GO.txt
- Go Results as Excel: Media:Increased_LH_20131015-Criterion0-GO.xls
- MAPP: not an uploadable file type, see screen shot above
- The MAPPFinder GO mappings file: Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.gmf
