Anuvarsh Week 9 - Revision history

Anuvarsh: /* Coloring a MAPP with expression data */ added procedure followed

2015-11-04T04:46:51Z

‎Coloring a MAPP with expression data: added procedure followed

Anuvarsh: /* Creating an Expression Dataset in the Expression Dataset Manager */ added procedure followed

2015-11-04T04:42:44Z

‎Creating an Expression Dataset in the Expression Dataset Manager: added procedure followed

Anuvarsh: /* Putting a gene on the MAPP using the GeneFinder window */ added procedure followed

2015-11-04T04:40:10Z

‎Putting a gene on the MAPP using the GeneFinder window: added procedure followed

Anuvarsh: /* Compare Gene Database to Outside Resource */ deleted the extra section

2015-11-04T04:32:13Z

‎Compare Gene Database to Outside Resource: deleted the extra section

← Older revision		Revision as of 04:46, 4 November 2015
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	===Coloring a MAPP with expression data===		===Coloring a MAPP with expression data===
		+	*I launched the MAPPFinder program from within GenMAPP by selecting MAPPFinder under the Tools menu on GenMAPP
		+	*After ensuring that the Gene Database for the correct species was loaded, I selected the button "Calculate New Results"
		+	*I clicked on "Find File" and selected the .gex file that contained my Expression Dataset (This file can be found in the .zip file at the beginning of this journal)
		+	*I chose the LogFoldChange color set and the Increased criteria in the right-hand box, and selected the boxes for "Gene Ontology" and "p value"
		+	*I then named my results file "MAPPFinder-Results-20151102_AV", and clicked Run MAPPFinder. MAPPFinder took several seconds to run. After MAPPFinder finishes running, a Gene Ontology browser opened showing my results.

	Note: When I double click on one of the GO terms to open the data in GenMAPP, I get the following error:<br>		Note: When I double click on one of the GO terms to open the data in GenMAPP, I get the following error:<br>

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 ===Creating an Expression Dataset in the Expression Dataset Manager===
 * How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset.  Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?
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 **5,221 IDs were imported with the new database. This is the same as the number of IDs imported with the 2010 database.
 **All of the Errors in the .EX.txt file said: "Gene not found in OrderedLocusNames or any related system."
-**I opened the .EX.txt file and searched for the genes that were documented with an error in the "Uniprot" table in the database file via Microsoft Access. I spot checked 6 genes ("VC2209
+**I opened the .EX.txt file and searched for the genes that were documented with an error in the "Uniprot" table in the database file via Microsoft Access. I spot checked 6 genes ("VC2209", "VCA1031", "VCA0745", "VC1476", "VCA0534", "VCA0276") and noticed that none of these genes appeared in the "Uniprot" table in the database. Because of this, I can conclude that these genes were not present in the UniProt XML.
 ", "VCA1031", "VCA0745", "VC1476", "VCA0534", "VCA0276") and noticed that none of these genes appeared in the "Uniprot" table in the database. Because of this, I can conclude that these genes were not present in the UniProt XML.
 ===Coloring a MAPP with expression data===

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 ===Putting a gene on the MAPP using the GeneFinder window===
-* Tried a "" from each of the gene ID systems. Open the Backpage and saw that all of the cross-referenced IDs that are supposed to be there are there.<br>
+* In the main GenMAPP Drafting Board window, I left-clicked on the icon for "Gene" in the upper left corner of the window.  I clicked on the Drafting Board to place the Gene on the MAPP.  Then, I right-clicked on the gene to access the GeneFinder window.  I pasted "VC_0014" into the Gene ID field, and selected the OrderedLocusNames ID.  Once the ID was found, I clicked on the OK button to return to the Drafting Board window.
 [[Image:Gene-Finder-Results-AV.png]]
 ===Creating an Expression Dataset in the Expression Dataset Manager===

← Older revision		Revision as of 04:32, 4 November 2015
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	Note: Once again, there are several differences between GO terms between the top ranked GO terms from the 2015 database and those found in the 2010 and 2009 version of the V. cholera database. These differences, as explained in the week 8 journal, are most likely due to new information made available through UniProt, GO, and GOA.		Note: Once again, there are several differences between GO terms between the top ranked GO terms from the 2015 database and those found in the 2010 and 2009 version of the V. cholera database. These differences, as explained in the week 8 journal, are most likely due to new information made available through UniProt, GO, and GOA.

−	~~== Compare Gene Database to Outside Resource==~~

−	The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.
−
−	Note: I am unsure how to search the UniProt XML page for the gene IDs as it is not in any table format. More analysis is required. Will come back to this after clarification from Dr. Dionisio or Dr. Dahlquist.

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