Difference between revisions of "Vpachec3 Week 15"

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(→‎MAPPFinder Procedure: edited wording)
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=== MAPPFinder Procedure ===
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== MAPPFinder Procedure ==
 
# MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
 
# MAPPFinder was launched from the GenMAPP window: "Tools" > "MAPPFinder".
 
# 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 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.
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# "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.
 
# "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.
  
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=== Filtered GO List ===
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'''BEFORE creating the mapp, we wanted to filter the GO terms in excel to narrow down which pathway we would want to map out.'''
  
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== Filtered GO List ==
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DECREASED INFO
 
*The GO term files above were opened in Excel, and the following filters were placed on the given columns:
 
*The GO term files above were opened in Excel, and the following filters were placed on the given columns:
 
** Z score: greater than 2
 
** Z score: greater than 2
 
** PermuteP: less than 0.05
 
** PermuteP: less than 0.05
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** Number changed: greater than or equal to 4 AND less than 100
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** Number changed: greater than or equal to 5 AND less than 100
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** Percent changed: great than or equal to 15
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** Percent changed: great than or equal to 25
 
* Values in the following columns were recorded:
 
* Values in the following columns were recorded:
 
** Number Changed
 
** Number Changed
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** PermuteP
 
** PermuteP
 
** AdjustedP
 
** AdjustedP
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* 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.
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* Some of the above filter criteria had to be adjusted to attain 16 non-redundant GO terms.  
  
 
==MAPP Making==
 
==MAPP Making==
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TO DO
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* We decided to map the pathway of oxidative phosphorylation. We chose this because on it was on the list of the top ten GO terms for decreased. Also, Van Acker et al (2013) referenced that they noticed a decrease in the electron transport chain and part of this correlation was with the oxidative phosphorylation pathway.
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* Using the Kegg [http://www.genome.jp/kegg/pathway.html] website, we were able to look up our bacteria, ''Burkholderia cenocepcia J2315'' and found the oxidative phosphorylation pathway.
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[File:Screen Shot 2015-12-14 at 11.10.55 PM.png]
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 +
 
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We wanted to mirror the format of this page, as much as we possibly could, in GenMAPP to see our results in whether the genes in this pathway was decreased. We predicted that the genes should be decreased because of the results provided in the paper and more so in our GO terms.
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[File:Oxphosmapp.png]
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 +
 
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Our map shows that the genes were in fact decreased.
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 +
 
 +
 
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==Sanity Check Table Update==
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There was also a new sanity check table made to summarize the different p-values tested. We decided to use the BH pvalue and the table highlights the other possibilities of criteria. Kevin [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Kevin_Wyllie_Week_15] had the table on his page.
  
 
==Links==
 
==Links==

Revision as of 07:17, 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.

BEFORE creating the mapp, we wanted to filter the GO terms in excel to narrow down which pathway we would want to map out.


Filtered GO List

DECREASED INFO

  • 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 5 AND less than 100
    • Percent changed: great than or equal to 25
  • 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.

MAPP Making

  • We decided to map the pathway of oxidative phosphorylation. We chose this because on it was on the list of the top ten GO terms for decreased. Also, Van Acker et al (2013) referenced that they noticed a decrease in the electron transport chain and part of this correlation was with the oxidative phosphorylation pathway.
  • Using the Kegg [1] website, we were able to look up our bacteria, Burkholderia cenocepcia J2315 and found the oxidative phosphorylation pathway.

[File:Screen Shot 2015-12-14 at 11.10.55 PM.png]


We wanted to mirror the format of this page, as much as we possibly could, in GenMAPP to see our results in whether the genes in this pathway was decreased. We predicted that the genes should be decreased because of the results provided in the paper and more so in our GO terms.

[File:Oxphosmapp.png]


Our map shows that the genes were in fact decreased.



Sanity Check Table Update

There was also a new sanity check table made to summarize the different p-values tested. We decided to use the BH pvalue and the table highlights the other possibilities of criteria. Kevin [2] had the table on his page.

Links

Vpachec3 User Page

Vpachec3 User Page

GÉNialOMICS Links

Weekly Group Assignments Shared Group Journals Project Links Team Members
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