Difference between revisions of "Lena Week 8"

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=='''Part 1'''==
 
=='''Part 1'''==
 
:
 
:
−
:[[Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20091014.xls]]
+
:[[Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20131015.txt ‎]]
−
:[[Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20091014.txt ‎]]
+
:[[Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20131015.xls ‎]]
 +
:
 +
:When Filtered p-value less than 0.05, 948 total results found.
  
 
=='''Part 2'''==
 
=='''Part 2'''==
 +
===GenMAPP Expression Dataset Manager Procedure===
 
:
 
:
 
*I used the 2009 version of the ''Vibrio cholerae'' Gene Database with GenMAPP.
 
*I used the 2009 version of the ''Vibrio cholerae'' Gene Database with GenMAPP.
Line 11: Line 14:
 
*The exception file was saved here. [[Media:Merrell_Compiled_Raw_Data_Vibrio_AJV.EX.txt]]
 
*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.
 
*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 had more errors than my partner who was using the updated version, she has 121.  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.
 +
:[[Image:Capture1.PNG]]
 +
 +
:
 +
*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.  [[Image:Capture5.PNG]]
 +
*We had very different lists of top 10 GO terms.  Her's is probably more accurate since it is the updated version.
 +
:
 +
*I searched GO terms associated with the genes mentioned by Merrel et al.
 +
**VC0028: metal ion binding, iron-sulfur cluster binding, 4 iron, 4 sulfur cluster binidng, catalytic activity
 +
**VC0941: transferase activity, glycine hydroxymethyltranserase activity, lygase activity, dihydroxy-acid dehydrase activity,
 +
**VC0869: catalytic activity, ligase activity,phosphoriboseylformylglycinamide synthase activity
 +
**VC0051: nucleotide binding, ATP binding, catalytic activity, lyase activity, carboxy-lyase activity, phosphoribosylaminoimidazole carboxylase activity,
 +
**VC0647: nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity, transferase activity, 3'-5' exoribonuclease activity, RNA binding, mitochondrion
 +
**VC2350: deoxyribose-phosphate aldolase activity, lyase activity, catalytic activity
 +
**VCA0583: outer membrane-bounded periplasmic space
 +
*My buddy and I had different terms associated with the genes.  Since the last update, more terms were added for 2010.
 +
:
 +
* I clicked on the GO term nucleotidyltransferase activity and this window came up.  There were significant decreases in  six places for VC0647.  [[Image:Nucleotydal_transferase.PNG]]
 +
:
 +
====Gene: PNP_VIBCH====
 +
:
 +
*I doubled clicked on the gene PNP_VIBCH and was directed to this webpage.  The function of this gene is to aid in mRNA degredation.
 +
:[[Image:Capture.PNG]]
 +
 +
===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]]
 +
 +
Created by [[User:Lena|Lena Hunt]]

Latest revision as of 05:00, 18 October 2013

Contents

[edit] Part 1

Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20131015.txt ‎
Media: Merrell_Compiled_Raw_Data_Vibrio_LH_20131015.xls ‎
When Filtered p-value less than 0.05, 948 total results found.

[edit] Part 2

[edit] 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 121. 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.
Capture1.PNG

[edit] 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...
  1. Transport Activity
  2. Localization
  3. Macromolecule Metabolic Process
  4. Cellular Macromolecule Metabolic Process
  5. Cellular Bipolymer Biosnythetic Process
  6. Bipolymer Biosnythetic Process
  7. Bipolymer Metabolic Process
  8. Amino Acid Metabloic Process
  9. Cellular Amino Acid and Derivative Metabolic Process
  10. Cellular Nitrogen Compound Metabolic Process
  • Here is an image of the results. Capture5.PNG
  • We had very different lists of top 10 GO terms. Her's is probably more accurate since it is the updated version.
  • I searched GO terms associated with the genes mentioned by Merrel et al.
    • VC0028: metal ion binding, iron-sulfur cluster binding, 4 iron, 4 sulfur cluster binidng, catalytic activity
    • VC0941: transferase activity, glycine hydroxymethyltranserase activity, lygase activity, dihydroxy-acid dehydrase activity,
    • VC0869: catalytic activity, ligase activity,phosphoriboseylformylglycinamide synthase activity
    • VC0051: nucleotide binding, ATP binding, catalytic activity, lyase activity, carboxy-lyase activity, phosphoribosylaminoimidazole carboxylase activity,
    • VC0647: nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity, transferase activity, 3'-5' exoribonuclease activity, RNA binding, mitochondrion
    • VC2350: deoxyribose-phosphate aldolase activity, lyase activity, catalytic activity
    • VCA0583: outer membrane-bounded periplasmic space
  • My buddy and I had different terms associated with the genes. Since the last update, more terms were added for 2010.
  • I clicked on the GO term nucleotidyltransferase activity and this window came up. There were significant decreases in six places for VC0647. Nucleotydal transferase.PNG

[edit] Gene: PNP_VIBCH

  • I doubled clicked on the gene PNP_VIBCH and was directed to this webpage. The function of this gene is to aid in mRNA degredation.
Capture.PNG

[edit] Uploaded Files

Created by Lena Hunt

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Lena_Week_8&oldid=3532"
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