Difference between revisions of "Individual hw week 8"
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the top 10 gene ontology terms were | the top 10 gene ontology terms were | ||
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1.Protein folding | 1.Protein folding | ||
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2.Chorismate metabolic process | 2.Chorismate metabolic process | ||
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3.aromatic amino acid biosynthesis process | 3.aromatic amino acid biosynthesis process | ||
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4. cytoplasm | 4. cytoplasm | ||
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5.protein-N(PI)-phosphohistidine-sugar phosphotransferase activity | 5.protein-N(PI)-phosphohistidine-sugar phosphotransferase activity | ||
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6.solute:hydrogen symporter activity | 6.solute:hydrogen symporter activity | ||
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7.sugar:hydrogen symporter activity | 7.sugar:hydrogen symporter activity | ||
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8.cation:sugar symporter activity | 8.cation:sugar symporter activity | ||
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9.phosphoenolpyruvate-dependent sugar phosphotransferase system | 9.phosphoenolpyruvate-dependent sugar phosphotransferase system | ||
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10.zinc ion binding | 10.zinc ion binding | ||
| + | When I compared my list to stephen's it was apparent that they were different. I believe that this difference arises from the different versions of the data that we used. Mine was from 2009 and his was from 2010. | ||
| + | |||
| + | ===GO Search=== | ||
| + | |||
| + | VC0647- 3'-5' exoribonuclease activity | ||
| + | VCA0583- outer membrane-bounded periplasmic space | ||
| + | |||
| + | I looked up the genes associated with VC0647 and chose the gene DSBA_VIBCH. This gene encodes for Thiol:Disulfate interchange protein. This gene's expression increased during this experiment. This protein is responsible for the formation of disulfide bonds.This protein is useful for its involvement in the secretion of virulence factors. | ||
| + | [[Media:VC0467_MPM.zip]] | ||
| + | |||
| + | ===Data Analysis=== | ||
| + | |||
| + | It appears that the increased amount of cellular activity in the pathogenic strain compared to the normal strain is all geared towards cell growth and division. There is an increase in the carbohydrate transporters which means an increased up take of glucose for metabolism. There is also a lot of membrane activity going on in the pathogenic strain which would make sense if the bacterium is growing and dividing because membranes are essential for the cellular envelope. The increase in hydrogen symporter activity could have to do with creating some sort of electro-chemical concentration gradient. Most of the other increased activity has to do with some aspect of DNA replication or protein synthesis. | ||
| + | |||
| + | [[Media:Improved_MAPPFinder_GO.txt_excel_file_MPM.xls]]<br> | ||
[[Media:Increased_MPM-Criterion1-GO.txt]]<br> | [[Media:Increased_MPM-Criterion1-GO.txt]]<br> | ||
| − | [[Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gex]] | + | [[Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gex]]<br> |
| + | [[Media:MAPPFinder_GO.txt_excel_file_MPM.xls]]<br> | ||
| + | [[Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.EX.txt]]<br> | ||
| + | [[Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gmf]]<br> | ||
| + | |||
[[Main Page]] | [[Main Page]] | ||
[[User:Mmalefyt|User Page]] | [[User:Mmalefyt|User Page]] | ||
[[Category:Journal Entry]] | [[Category:Journal Entry]] | ||
Latest revision as of 17:34, 17 October 2013
part 1 text file
Media:Merrell Compiled Raw Data Vibrio MPM.txt
Part 1 excel file
Media:Merrell_Compiled_Raw_Data_Vibrio_MPM.xls
948 results
During this lab I mapped the increased expression on the 2009 gene database. For some reason in the beginning of this assignment my .txt file did not want to load so I used my partner's
the top 10 gene ontology terms were
1.Protein folding
2.Chorismate metabolic process
3.aromatic amino acid biosynthesis process
4. cytoplasm
5.protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
6.solute:hydrogen symporter activity
7.sugar:hydrogen symporter activity
8.cation:sugar symporter activity
9.phosphoenolpyruvate-dependent sugar phosphotransferase system
10.zinc ion binding
When I compared my list to stephen's it was apparent that they were different. I believe that this difference arises from the different versions of the data that we used. Mine was from 2009 and his was from 2010.
[edit] GO Search
VC0647- 3'-5' exoribonuclease activity VCA0583- outer membrane-bounded periplasmic space
I looked up the genes associated with VC0647 and chose the gene DSBA_VIBCH. This gene encodes for Thiol:Disulfate interchange protein. This gene's expression increased during this experiment. This protein is responsible for the formation of disulfide bonds.This protein is useful for its involvement in the secretion of virulence factors. Media:VC0467_MPM.zip
[edit] Data Analysis
It appears that the increased amount of cellular activity in the pathogenic strain compared to the normal strain is all geared towards cell growth and division. There is an increase in the carbohydrate transporters which means an increased up take of glucose for metabolism. There is also a lot of membrane activity going on in the pathogenic strain which would make sense if the bacterium is growing and dividing because membranes are essential for the cellular envelope. The increase in hydrogen symporter activity could have to do with creating some sort of electro-chemical concentration gradient. Most of the other increased activity has to do with some aspect of DNA replication or protein synthesis.
Media:Improved_MAPPFinder_GO.txt_excel_file_MPM.xls
Media:Increased_MPM-Criterion1-GO.txt
Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gex
Media:MAPPFinder_GO.txt_excel_file_MPM.xls
Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.EX.txt
Media:Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gmf
