Difference between revisions of "Vpachec3 Week 15"

From LMU BioDB 2015
Jump to: navigation, search
(added new setions)
(→‎MAPPFinder Procedure: edited wording)
Line 1: Line 1:
 
=== MAPPFinder Procedure ===
 
=== MAPPFinder Procedure ===
 
# MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
 
# MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
−
# "Calculate New Results" was selected from the MAPPFinder window.
+
# Since the criterion for the Expression Dataset file was already made. We were able to choose this file for the set criterion and our .gbd file was already located in GenMAPP.
−
# Since the .gex file was already generated last week, "Find File" was selected and in the directory.
+
# Under the "Select Color Set" field, "KWVP_20151205" was selected.
−
# Under the "Select Color Set" field, "KWVP_20151205" was selected (the color set's name in this case is the same as the .gex file's name - and there's only one color set in the .gex file).
+
# After the color set has been selected, under the "Select Criteria to filter by" field, either increase or decrease was chosen. I did decreased and Kevin did increased.  
−
# After the color set has been selected, under the "Select Criteria to filter by" field, either increase or decrease was chosen.  
+
 
# The boxes for "Gene Ontology" and "Click here to calculate p values..." were checked.
 
# The boxes for "Gene Ontology" and "Click here to calculate p values..." were checked.
 
# The location to save the resulting .txt file was selected with the "Browse" option toward the bottom of the window.  
 
# The location to save the resulting .txt file was selected with the "Browse" option toward the bottom of the window.  
−
# "Run MAPPFinder" was selected to generate the gene ontology tree (and the aforementioned .txt files).
+
# "Run MAPPFinder" was selected to generate the gene ontology. When we clicked on the tree for a given term there should have been a mapp generated. However, the program was not responding, thus we had to make our own map.
−
#* The files generated can be found here:
+
−
#** [[media:KWVP_MAPPfinder_20151208-decrease-GO.txt|For downregulated GO terms.]]
+
−
#** [[media:KWVP_MAPPfinder_20151208-increase-GO.txt|For upregulated GO terms.]]
+
  
 
=== Filtered GO List ===
 
=== Filtered GO List ===

Revision as of 06:46, 15 December 2015

MAPPFinder Procedure

  1. MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
  2. Since the criterion for the Expression Dataset file was already made. We were able to choose this file for the set criterion and our .gbd file was already located in GenMAPP.
  3. Under the "Select Color Set" field, "KWVP_20151205" was selected.
  4. After the color set has been selected, under the "Select Criteria to filter by" field, either increase or decrease was chosen. I did decreased and Kevin did increased.
  5. The boxes for "Gene Ontology" and "Click here to calculate p values..." were checked.
  6. The location to save the resulting .txt file was selected with the "Browse" option toward the bottom of the window.
  7. "Run MAPPFinder" was selected to generate the gene ontology. When we clicked on the tree for a given term there should have been a mapp generated. However, the program was not responding, thus we had to make our own map.

Filtered GO List

  • The GO term files above were opened in Excel, and the following filters were placed on the given columns:
    • Z score: greater than 2
    • PermuteP: less than 0.05
    • Number changed: greater than or equal to 4 AND less than 100
    • Percent changed: great than or equal to 15
  • Values in the following columns were recorded:
    • Number Changed
    • Number Measured
    • Number in GO
    • Percent Changed
    • Percent Present
    • PermuteP
    • AdjustedP
  • Some of the above filter criteria had to be adjusted to attain 16 non-redundant GO terms. A list of these terms is shown below. For those terms which did not exactly fit this initial criteria, the altered criteria is apparent in the values on the table.

MAPP Making

TO DO

Links

Vpachec3 User Page

Vpachec3 User Page

GÉNialOMICS Links

Weekly Group Assignments Shared Group Journals Project Links Team Members
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Vpachec3_Week_15&oldid=7909"