Nanguiano Week 8 - Revision history

Nanguiano: /* Files as of 10/22/15 */ added GO and MAPPFinder files

2015-10-22T22:58:14Z

‎Files as of 10/22/15: added GO and MAPPFinder files

2015-10-22T22:55:50Z

‎MAPPFinder Procedure: finished using genmapp. rest of stuff is excel stuff

2015-10-22T22:40:23Z

‎MAPPFinder Procedure: added rest of go terms

2015-10-22T22:33:07Z

‎GenMAPP Expression Dataset Manager Procedure: minor wording change

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 * [[Media:Merrell_Compiled_Raw_Data_Vibrio_NA_20151015_Expression_ColorSet.gex | Expression Color Set]]
 <!-- [[File:Merrell_Compiled_Raw_Data_Vibrio_NA_20151015_Expression_ColorSet.gex]] -->
 === Normalize the log ratios for the set of slides in the experiment ===

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 *** GO Terms: transport, outer membrane-bounded periplasmic space, transporter activity
 * The GO Terms I found were not the same as the ones my partner found. <!-- why or why not? -->
 * Launch Microsoft Excel.  Open the copies of the .txt files in Excel (you will need to "Show all files" and click "Finish" to the wizard that will open your file).  This will show you the same data that you saw in the MAPPFinder Browser, but in tabular form.
 * Look at the top of the spreadsheet.  There are rows of information that give you the background information on how MAPPFinder made the calculations.  '''Compare this information with your partner who used a different version of the Vibrio Gene Database.  Which numbers are different?  Why are they different?  Record this information in your individual journal entry.'''

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 ** VC0869:
 *** GO Terms: glutamine metabolic process, purine nucleotide biosynthetic process, 'de novo' IMP biosynthetic process, cytoplasm, nucleotide binding, ATP binding, catalytic activity, ligase activity, phosphoribosylformyglycinamidine synthase activity
 * Click on one of the GO terms that are associated with one of the genes you looked up in the previous step. A MAPP will open listing all of the genes (as boxes) associated with that GO term. The genes named within the map are based on the UniProt identification system. To match the gene of interest to its identification go to the [http://www.uniprot.org/ UniProt site] and type in your gene ID into the search bar. Moreover, the genes on the MAPP will be color-coded with the gene expression data from the microarray experiment.  '''List in your journal entry the name of the GO term you clicked on and whether the expression of the gene you were looking for changed significantly in the experiment.'''
 ** Double-click on the gene box.  This will open a Internet Explorer window called the "Backpage" for this gene.  This page has links to pages for this gene in the public databases.  '''Click on the links to find out the function of this gene and record your answer in your individual journal page.'''

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 ** The file reported '''121 errors'''.
 *** In the EX.txt file, I opened it in excel and filtered by the "~Errors~" column. All 121 errors had the error message "Gene not found in OrderedLocusNames or any related system."
-*** My partner, Emily Simso, had 772 errors. This is likely due to the names that were used for the genes. Since the file I used was newer, it's possible that the gene names were changed.
+*** My partner, Emily Simso, had 772 errors. This is likely due to the names that were used for the genes. Since the file I used was newer, it's possible that the gene names were changed. Additionally, since the file I'm using was created by Dr. Dahlquist and Dr. Dionisio, it's possible that they knew the proper names and protocol to use to ensure the most successful files.
 * Now, I needed to customize the color set for GenMAPP. Under the "Color Sets" "Name" header, I named it "Significant Genes" and selected "Avg_LogFC_All" under the Gene Value dropdown. I created two criterion that I was going to color:
 ** "Increased": [Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05