Difference between revisions of "Anuvarsh Week 8"
From LMU BioDB 2015
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**This difference in errors is most likely due to the extensiveness of our databases. Because Brandon was using an older version of the database while I was using a newer version, it is possible that his version had fewer genes than mine. | **This difference in errors is most likely due to the extensiveness of our databases. Because Brandon was using an older version of the database while I was using a newer version, it is possible that his version had fewer genes than mine. | ||
*We produced our color set to indicate increased expression. | *We produced our color set to indicate increased expression. | ||
| + | *Top 10 Gene Ontology Results: | ||
| + | *#branched chain family amino acid metabolic process | ||
| + | *#branched chain family amino acid biosynthetic process | ||
| + | *#IMP metabolic process | ||
| + | *#IMP biosyntehtic process | ||
| + | *#purine ribonucleoside monophosphate metabolic process | ||
| + | *#purine nucleoside monophosphate metabolic process | ||
| + | *#purine nucleoside monophosphate biosyntehtic process | ||
| + | *#purine ribonucleoside monophosphate biosyntehtic process | ||
| + | *#arginine metabolic process | ||
| + | *#ccellular nitrogen compound biosynthetic process | ||
| + | *Searching through MAPPFinder for published genes: | ||
| + | **VC0028: metal ion binding, iron-sulfur cluster binding, 4 iron 4 sulfur cluster binding, catalytic activity, lyase activity | ||
| + | **VC0941: pyridoxal phosphate binding, catalytic activity, transferase activity, glycine hydroxymethyltransferase activity | ||
| + | **VC0869: nucleotide binding, ATP binding, catalytic activity, lyase activity | ||
| + | **VC0051: nucleotide binding, ATP binding, catalytic activity, lyase activity, carboxy-lyase activity | ||
| + | **VC0647: 3'-5'-exoribonuclease activity, transferase activity, nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity | ||
| + | **VC0468: metal ion binding, nucleotide binding, ATP binding, catalytic activity, ligase activity, glytathione synthase activity | ||
| + | **VC2350: catalytic activity, lyase activity, deoxyribose-phosphate aldolase activity | ||
| + | **VCA0583: outer membrane-bounded periplasmic space | ||
{{Template:Anuvarsh}} | {{Template:Anuvarsh}} | ||
Revision as of 22:53, 22 October 2015
Contents
Electronic Lab Notebook
- Part 1 Spreadsheet from Class on 10/15/2015
- Part 2 Text File from Class on 10/20/2015
- Exceptions List from Raw Data Conversion on GenMAPP
- GenMAPP generated file after uploading data
Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)
MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)
Reminders
- Finish the Sanity Check
- I used the 2010 Vibrio Cholera database
- When uploading my tab delimited file to the GenMAPP software for conversion, 121 errors were detected in my raw data.
- My partner, Brandon L., had 772 errors detected in his raw data conversion while using the 2009 Vibrio Cholera database.
- This difference in errors is most likely due to the extensiveness of our databases. Because Brandon was using an older version of the database while I was using a newer version, it is possible that his version had fewer genes than mine.
- We produced our color set to indicate increased expression.
- Top 10 Gene Ontology Results:
- branched chain family amino acid metabolic process
- branched chain family amino acid biosynthetic process
- IMP metabolic process
- IMP biosyntehtic process
- purine ribonucleoside monophosphate metabolic process
- purine nucleoside monophosphate metabolic process
- purine nucleoside monophosphate biosyntehtic process
- purine ribonucleoside monophosphate biosyntehtic process
- arginine metabolic process
- ccellular nitrogen compound biosynthetic process
- Searching through MAPPFinder for published genes:
- VC0028: metal ion binding, iron-sulfur cluster binding, 4 iron 4 sulfur cluster binding, catalytic activity, lyase activity
- VC0941: pyridoxal phosphate binding, catalytic activity, transferase activity, glycine hydroxymethyltransferase activity
- VC0869: nucleotide binding, ATP binding, catalytic activity, lyase activity
- VC0051: nucleotide binding, ATP binding, catalytic activity, lyase activity, carboxy-lyase activity
- VC0647: 3'-5'-exoribonuclease activity, transferase activity, nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity
- VC0468: metal ion binding, nucleotide binding, ATP binding, catalytic activity, ligase activity, glytathione synthase activity
- VC2350: catalytic activity, lyase activity, deoxyribose-phosphate aldolase activity
- VCA0583: outer membrane-bounded periplasmic space
Other Links
User Page: Anindita Varshneya
Class Page: BIOL/CMSI 367: Biological Databases, Fall 2015
Group Page: GÉNialOMICS
Assignment Pages
Week 1 Assignment
Week 2 Assignment
Week 3 Assignment
Week 4 Assignment
Week 5 Assignment
Week 6 Assignment
Week 7 Assignment
Week 8 Assignment
Week 9 Assignment
Week 10 Assignment
Week 11 Assignment
Week 12 Assignment
No Week 13 Assignment
Week 14 Assignment
Week 15 Assignment
Individual Journals
Individual Journal Week 2
Individual Journal Week 3
Individual Journal Week 4
Individual Journal Week 5
Individual Journal Week 6
Individual Journal Week 7
Individual Journal Week 8
Individual Journal Week 9
Individual Journal Week 10
Individual Journal Week 11
Individual Journal Week 12
Individual Journal Week 14
Individual Journal Week 15
Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
GÉNialOMICS Journal Week 10
GÉNialOMICS Journal Week 11
GÉNialOMICS Journal Week 12
GÉNialOMICS Journal Week 14
GÉNialOMICS Journal Week 15
