Difference between revisions of "Blitvak Week 8"
From LMU BioDB 2015
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==Week 8 Individual Journal== | ==Week 8 Individual Journal== | ||
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| + | ===DNA Microarray Analysis part 1=== | ||
| + | *[http://www.openwetware.org/images/d/d6/Merrell_Compiled_Raw_Data_Vibrio.xls Merrell_Compiled_Raw_Data_Vibrio.xls] was downloaded and opened with Excel | ||
| + | * | ||
*[[Media:Merrell_Compiled_Raw_Data_Vibrio_BL_20151015.xls|Modified Excel File/Data]] | *[[Media:Merrell_Compiled_Raw_Data_Vibrio_BL_20151015.xls|Modified Excel File/Data]] | ||
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*[[Media:Merrell_Compiled_Raw_Data_Vibrio_BL_20151015.txt|For GenMAPP]] | *[[Media:Merrell_Compiled_Raw_Data_Vibrio_BL_20151015.txt|For GenMAPP]] | ||
| − | + | [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020090622/Vc-Std_External_20090622.zip/download Working with: 2009 Vibrio Cholera database] | |
*772 errors were detected in the raw data by genMAPP using the 2009 database | *772 errors were detected in the raw data by genMAPP using the 2009 database | ||
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==Results of 10/22 Work Session== | ==Results of 10/22 Work Session== | ||
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| + | *'''Top 10 Ranked GO Terms''' | ||
| + | #macromolecule metabolic process | ||
| + | #localization | ||
| + | #transporter activity | ||
| + | #cellular macromolecule metabolic process | ||
| + | #transport | ||
| + | #establishment of localization | ||
| + | #cell projection organization | ||
| + | #cellular biopolymer metabolic process | ||
| + | #macromolecule biosynthetic process | ||
| + | #biopolymer metabolic process | ||
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*Analysis of the .EX.txt file produced by GenMAPP, via Excel, revealed that the 772 errors were: ''Gene not found in OrderedLocusNames or any related system''; this suggests that the 2009 database did not | *Analysis of the .EX.txt file produced by GenMAPP, via Excel, revealed that the 772 errors were: ''Gene not found in OrderedLocusNames or any related system''; this suggests that the 2009 database did not | ||
Revision as of 22:35, 22 October 2015
Contents
Week 8 Individual Journal
DNA Microarray Analysis part 1
- Merrell_Compiled_Raw_Data_Vibrio.xls was downloaded and opened with Excel
Working with: 2009 Vibrio Cholera database
- 772 errors were detected in the raw data by genMAPP using the 2009 database
- 121 errors were detected in the raw data by genMAPP using the 2010 database by my partner, Anindita V.
Results of 10/20 Work Session
Results of 10/22 Work Session
- Top 10 Ranked GO Terms
- macromolecule metabolic process
- localization
- transporter activity
- cellular macromolecule metabolic process
- transport
- establishment of localization
- cell projection organization
- cellular biopolymer metabolic process
- macromolecule biosynthetic process
- biopolymer metabolic process
- Analysis of the .EX.txt file produced by GenMAPP, via Excel, revealed that the 772 errors were: Gene not found in OrderedLocusNames or any related system; this suggests that the 2009 database did not
increased expression
Brandon Litvak
BIOL 367, Fall 2015
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