Ajvree Week 8
Part 1 In-Class Excel Text File:
Merrell_Compiled_Raw_Data_Vibrio_AJV.txt
Original Excel File:
Merrell_Compiled_Raw_Data_Vibrio_AJV.xls
When Filtered p-value less than 0.05, 948 results were found.
Errors found on txt file: 121
Partners errors: 772
My partner has more errors probably because it is an older database, and many of the errors were corrected in the next year's database.
Rows that had errors: VC2209 VC2209 VCA1031 VCA0745 VC1476 VCA0534 VCA0276 VCA0276 VC1660 VC2209 VC2209 VCA0449 VCA0745 VC1759 VCA0534 VCA0276 VCA0276 VCA0280 VC1018 VC1307 VC1513 VC2049 VC2049 VC2338 VC2338 VCA0596 VC0500 VC0518 VC0521 VC0793 VC1620 VC1620 VC1620 VC1625 VC1625 VC1018 VC1307 VC1513 VC1513 VC1807 VC2209 VC2049 VC2338 VC2338 VCA0596 VCA0358 VC0499 VC0501 VC0518 VC0521 VC0793 VC0793 VC0818 VC1620 VC1620 VC1620 VC1625 VC1625 VCA0133 VC0284 VC0284 VC0583 VC0607 VC1660 VC2209 VC2209 VCA0454 VCA1031 VCA1031 VCA1036 VCA1073 VCA1073 VCA0232 VCA0232 VC0663 VC2209 VCA1089 VCA1104 VC0284 VC0284 VC0583 VC0607 VC1395 VC1660 VC2209 VC2209 VC2209 VCA1031 VCA1036 VCA1073 VCA1073 VCA0232 VC1476 VCA1089 VCA1104 VC1807 VC2109 VCA0596 VCA0887 VC1620 VC1620 VC1620 VC2437 VC2700 VC2700 VCA0674 VCA0692 VCA0938 VC1018 VC2109 VCA0887 VC0254 VC0518 VC1620 VC1620 VC2437 VC2700 VC2700 VC2700 VCA0674 VCA0692
Merrell_Compiled_Raw_Data_Vibrio_AJV_20131015.EX.txt
Top ten gene ontology results:
1) branched chain family amino acid metabolic process
2)branched chain family amino acid biosynthetic process
3)IMP metabolic process
4)IMP biosynthetic process
5)purine ribonucleoside monophosphate metabolic process
6)purine nucleoside monophosphate biosynthetic process
7)purine ribonucleoside monophosphate biosynthetic process
8)arginine metabolic process
9)cellular nitrogen compound biosynthetic process
10)ribonucleoside monophosphate biosynthetic process
Partner had different results. Since they had significantly more errors, it may have skewed the available data and changed the rankings.
Searched for: VC0028
GO terms associated with genes that were highlighted in blue:
-branched chain family amino acid biosynthetic process
-cellular amino acid biosynthetic process
-metabolic process
-metal ion binding
-iron sulfur cluster binding
-4 iron, 4 sulfur cluster binding
-catalytic activity
-lyase activity
-dihydroxy-acid dehydratase activity
Chosen GO term to click on: lyase activity
When typed in gene ID VC0028 to Uniprot, result given was dihydroxy-acid dehydratase protein for organism Vibrio cholerae serotype O1.
Had entry number Q9KVW0, ILVD_VIBCH
Gene listed as pink, so it increased during the experiment.
Double clicked on gene box to get "backpage," followed links to find out following information:
- catalytic activity
- metabolic processes that aid in growth of cell
- formation of amino acids
- catalytic activity involving cleavage of carbon bonds
- interaction/binding with metal ions
- interaction with iron and sulfur atoms
- interaction with 4Fe-4S clusters
Data Analysis
The genes that were found to be increased in the experiment primarily focused on the growth and enzymatic activity of the pathogenic cell. The importance of the pathogenic cell's ability to metabolize and interact is shown through the increase in GO terms such as "catalytic activity," "lyase activity," and "metabolic activity." If the cell is unable to perform these vital functions, it will be unable to be successfully pathogenic.
Increased_AJV-Criterion0-GO.txt
Merrell_Compiled_Raw_Data_Vibrio_AJV_20131015.gex
Increased_AJV-Criterion0-GO.xls
