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| | *Choose the Color Set and Criteria with which to filter the data. Click on "Decreased" criteria in the right-hand box. | | *Choose the Color Set and Criteria with which to filter the data. Click on "Decreased" criteria in the right-hand box. |
| | *Check the boxes next to "Gene Ontology" and "p value". | | *Check the boxes next to "Gene Ontology" and "p value". |
| − | *Click the "Browse" button and create a meaningful filename for your results (ex. "Merrell_Data_Vibrio_MAPPFinder_Decreased_KS_20131010"). | + | *Click the "Browse" button and create a meaningful filename for your results (ex. "Merrell_Vibrio_Data_MAPPFinder_Analysis_Decreased_KS_20131017"). |
| | *Click "Run MAPPFinder". | | *Click "Run MAPPFinder". |
| | [[Image:GenMAPP Screenshot MAPPFinder Select Criterion to Calculate Results KS 20131017.jpg|thumb|none|upright=3.5]] | | [[Image:GenMAPP Screenshot MAPPFinder Select Criterion to Calculate Results KS 20131017.jpg|thumb|none|upright=3.5]] |
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| | ::*'''The screenshot below shows the top 10 Gene Ontology terms from the results:''' | | ::*'''The screenshot below shows the top 10 Gene Ontology terms from the results:''' |
| | [[Image:MAPPFinder Screenshots Top 10 Gene Ontology Terms KS 20131017.jpg|thumb|none|upright=4]] | | [[Image:MAPPFinder Screenshots Top 10 Gene Ontology Terms KS 20131017.jpg|thumb|none|upright=4]] |
| | + | ::*No, my buddy and I did not have the same top 10 GO terms. From comparing the GO result text files (the process to obtain them is described in later steps) between the two of us, I believe that this is a result of a discrepancy in setting the criterion for decreased expression in the Expression Dataset Manager. |
| | *In the main MAPPFinder Browser window, click on the button "Collapse the Tree". Then, you can search for the genes that were mentioned by Merrell et al. (2002), VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583. | | *In the main MAPPFinder Browser window, click on the button "Collapse the Tree". Then, you can search for the genes that were mentioned by Merrell et al. (2002), VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583. |
| − | :*Type the identifier for one of these genes into the MAPPFinder browser gene ID search field. | + | :*Type the identifier of one of the genes into the MAPPFinder browser gene ID search field. |
| | :*Choose "OrderedLocusNames" from the drop-down menu to the right of the search field. | | :*Choose "OrderedLocusNames" from the drop-down menu to the right of the search field. |
| | :*Click on the GeneID Search button. The GO term(s) that are associated with that gene will be highlighted in blue. | | :*Click on the GeneID Search button. The GO term(s) that are associated with that gene will be highlighted in blue. |
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