Ksherbina Week 8 - Revision history

Ksherbina: /* MAPPFinder Procedure */

2013-10-18T08:38:16Z

‎MAPPFinder Procedure

2013-10-18T08:36:30Z

‎MAPPFinder Procedure: Added another sub-bullet

2013-10-18T08:28:19Z

‎MAPPFinder Procedure: Added a sub-bullet.

2013-10-18T08:22:18Z

‎Interpretation of GO Results: Added an interpretation of the GO results.

2013-10-18T08:07:21Z

‎MAPPFinder Procedure: Added another bullet. Added a subsection.

2013-10-18T07:46:20Z

‎Files generated in the above procedures: Added link to the filtered GO results

2013-10-18T07:43:27Z

‎MAPPFinder Procedure: Added instructions to filter the GO results.

2013-10-18T07:19:36Z

‎Files generated in the above procedures: Added link to the MAPPFinder GO mappings file.

2013-10-18T07:15:33Z

‎Files generated in the above procedures: Added link to the resulting file from using the Decreased criterion in MAPPFinder.

2013-10-18T07:11:57Z

‎MAPPFinder Procedure: Added bullet.

@@ Line 188: / Line 188: @@
 :*In the MAPP, double click on the box '''PNP_VIBCH'''.
 :*An Internet Explorer window will pop up that has links to different pages for the gene in public databases.
-::*'''The VC0647 gene is involved in mRNA degradation. It hydrolyzes single-stranded polyribunucleotides in the 3'-5' direction.'''
+::*'''The VC0647 gene is involved in mRNA degradation. It hydrolyzes single-stranded polyribunucleotides in the 3'-5' direction. (As described in the gene entry in UniProt.)'''
 *In Windows, make a copy of the results (i.e. Merrell_Vibrio_Data_MAPPFinder_Analysis_Decreased_KS_20131017-Criterion0-GO.txt) file.
 *Open the copy of the results file in Excel.

@@ Line 191: / Line 191: @@
 *In Windows, make a copy of the results (i.e. Merrell_Vibrio_Data_MAPPFinder_Analysis_Decreased_KS_20131017-Criterion0-GO.txt) file.
 *Open the copy of the results file in Excel.
 *Click on a cell in the row of headers. On the tool bar, select Sort & Filter > Filter. Set the following filters:
   Z Score (in column N) greater than 2

@@ Line 176: / Line 176: @@
 ::*'''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]]
 *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 of one of the genes into the MAPPFinder browser gene ID search field.

← Older revision		Revision as of 08:22, 18 October 2013
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	====Interpretation of GO Results====		====Interpretation of GO Results====
		+
		+	It would make sense that GO terms for intracellular transport are enriched for the pathogenic ''V. cholerae'' strain because its ability to infect a host cell is dependent upon its ability to transfer proteins to the host, such as transcriptional regulators that would influence the gene expression within the host. In addition, there are several GO terms relating to metabolism, such as glucose metabolic process, that were enriched in the pathogenic strain. This is expected because the pathogenic strain will not be able to live, reproduce, or respond to environmental stimuli without performing vital metabolic processes. Also, there are several GO terms relating to gene expression, specifically translation, that were enriched in the pathogenic strain. This is also makes sense because the pathogenic strain must be able to translate all of the proteins that is necessary for it to live and to reproduce so as it infect a host cell successfully.

	==Files generated in the above procedures==		==Files generated in the above procedures==

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   Percent Changed (in column L) greater than or equal to 25
 *Save the file as a different Excel spreadsheet named, for example "Merrell_Vibrio_Data_MAPPFinder_Analysis_Decreased_KS_20131017-Criterion0-GO_Filtered", by selecting File > Save As and select Excel workbook (.xls) from the drop-down menu.
 ==Files generated in the above procedures==

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 *[[Media:Merrell Compiled Raw Data Vibrio KS 20131010.gex|GEX file]].
 *[[Media:RNA processing KS 20131017.mapp|MAPP of RNA Proccessing]].
-*[[Media:Merrell Vibrio Data MAPPFinder Analysis Decreased KS 20131017-Criterion0-GO.txt|Criterion0-GO.txt file]].
+*[[Media:Merrell Vibrio Data MAPPFinder Analysis Decreased KS 20131017-Criterion0-GO.txt|GO results file]].
 :*From the way I performed the analysis, Criterion0 in this case refers to the "Decreased" criterion.
 *[[Media:Merrell Compiled Raw Data Vibrio KS 20131010.gmf|MAPPFinder GO mappings file]].
 [[Category:Journal Entry]]
 [[Category:Individual Homework]]

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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.
 *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".
 [[Image:GenMAPP Screenshot MAPPFinder Select Criterion to Calculate Results KS 20131017.jpg|thumb|none|upright=3.5]]
@@ Line 188: / Line 188: @@
 :*An Internet Explorer window will pop up that has links to different pages for the gene in public databases.
 ::*'''The VC0647 gene is involved in mRNA degradation. It hydrolyzes single-stranded polyribunucleotides in the 3'-5' direction.'''
 ==Files generated in the above procedures==