Vpachec3 Week 9 - Revision history

Vpachec3: /* Links */ Added template for journal links

2015-11-04T08:00:15Z

‎Links: Added template for journal links

Vpachec3: deleted section

2015-11-04T07:58:53Z

deleted section

Vpachec3: /* Coloring a MAPP with expression data */ added note

2015-11-04T07:58:25Z

‎Coloring a MAPP with expression data: added note

Vpachec3: /* Running MAPPFinder */ added screen shot

2015-11-04T07:57:37Z

‎Running MAPPFinder: added screen shot

Vpachec3: /* OriginalRowCounts Comparison */

2015-11-04T07:55:33Z

‎OriginalRowCounts Comparison

Vpachec3: /* Creating an Expression Dataset in the Expression Dataset Manager */ fixed the bolding

2015-11-04T07:55:09Z

‎Creating an Expression Dataset in the Expression Dataset Manager: fixed the bolding

Vpachec3: /* Creating an Expression Dataset in the Expression Dataset Manager */ Added answer

2015-11-04T07:54:30Z

‎Creating an Expression Dataset in the Expression Dataset Manager: Added answer

Vpachec3: /* Putting a gene on the MAPP using the GeneFinder window */ added note and screenshot

2015-11-04T07:49:43Z

‎Putting a gene on the MAPP using the GeneFinder window: added note and screenshot

@@ Line 189: / Line 189: @@
 ==Links==
 [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/User:Vpachec3 Vpachec3 User Page]
 [[Category: Journal Entry]]

← Older revision		Revision as of 07:58, 4 November 2015
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	[[File:Ontologyresultsmsvp.png]]		[[File:Ontologyresultsmsvp.png]]

−	~~== 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:~~

	==Links==		==Links==

@@ Line 180: / Line 180: @@
 ===Coloring a MAPP with expression data===
-Note:
+Note: This was the direction from week 8. I used the same coloring, increased red, decreased green and the same criterion.
 ===Running MAPPFinder===

@@ Line 183: / Line 183: @@
 ===Running MAPPFinder===
+[[File:Ontologyresultsmsvp.png]]
-Note:
-−
 == Compare Gene Database to Outside Resource==

@@ Line 136: / Line 136: @@
 Benchmark .gdb file: '''Vc-Std_External_20101022.gdb'''
-Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:In the gdb, we got the number 7664.
+'''Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:In the gdb, we got the number 7664.'''
 Note:

@@ Line 175: / Line 175: @@
 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?
-'''There 121 were errors. All of the errors were labeled “Gene not found in OrderedLocusNames or any related system.” This makes sense since I used the 2010 data last week and there was a 121 error message while my partner had a larger, 727. Also, we searched for that specific error labeled in the data set in last week's assignment as well so this is to be expected.
+'''There 121 were errors. All of the errors were labeled “Gene not found in OrderedLocusNames or any related system.” This makes sense since I used the 2010 data last week and there was a 121 error message while my partner had a larger, 727. Also, we searched for that specific error labeled in the data set in last week's assignment as well so this is to be expected.'''
-I searched using Acess through the UniProt table for VC2209 which had an error next to it. It was not found in the table, so the ID's that produced errors were not present in the UniProt XML.'''
+'''I searched using Acess through the UniProt table for VC2209 which had an error next to it. It was not found in the table, so the ID's that produced errors were not present in the UniProt XML.'''
 ===Coloring a MAPP with expression data===

@@ Line 167: / Line 167: @@
 * Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.
-Note:
+[[File:Vc0028msvp.png]]
 ===Creating an Expression Dataset in the Expression Dataset Manager===