Alex A. Cardenas Week 14: Difference between revisions
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==Electronic Notebook== | ==Electronic Notebook== | ||
*Computed the averages for A,B, and C along with multiplying all the c3/c5 by negative 1 | *Computed the averages for A,B, and C along with multiplying all the c3/c5 by negative 1. | ||
*Worked through the protocall and computed the Tstat values and the Pvalues along with changing some of the columns and rows. | |||
*Filtered out the Pvalue column to find how many genes Pvalues were less than 0.05, 0.01, and 0.001. | |||
**Pvalue < 0.05 - 680 genes. | |||
**Pvalue < 0.01 - 228 genes. | |||
**Pvalue < 0.001 - 26 genes. | |||
*The new spreadsheet can be found [[Media:AverageSpreadsheet.xlsx | here]]. | *The new spreadsheet can be found [[Media:AverageSpreadsheet.xlsx | here]]. | ||
*More modified spreadsheet can be found [[Media:AllSpreadsheet.xlsx | here]]. | *More modified spreadsheet can be found [[Media:AllSpreadsheet.xlsx | here]]. | ||
*When making the geneMAPP, there were 132 errors found but this is insignificant because this is out of 2740 genes. | |||
*geneMAPP excel file can be found [[Media:Mapfinderresults-Criterion1-GOrwaaa.xlsx | here]]. The text file for geneMAPP can be found [[Media:Mapfinderresults-Criterion1-GOrwaaaaaa.txt | here]]. | |||
*We looked at the top 10 genes with the lowest Pvalues, and the excel file can be found [[Media:TopTen.xlsx | here]]. | |||
*We also looked at the top 10 Gene Ontology terms and those can be found below. | |||
*#Pathogenesis | |||
*#Multi-organism process | |||
*#External encapsulating structure | |||
*#High-affinity iron ion transport | |||
*#Extracellular region | |||
*#Membrane Part | |||
*#Protein complex binding | |||
*#Immunoglobin binding | |||
*#Respiratory chain | |||
*#Periplasmic space | |||
*Top ten increasing GO terms looked at will be: | |||
*#amine biosynthetic process | |||
*#cellular amino acid biosynthetic process | |||
*#cellular nitrogen compound biosynthetic process | |||
*#antiport activity | |||
*#branched chain family amino acid metabolic process | |||
*#aspartate family amino acid metabolic process | |||
*#threonine metabolic process | |||
*#oxidation reduction | |||
*#vitamin binding | |||
*#oxidoreductace activity | |||
*Most Significant Genes | |||
*#SAR0633 - Q6GJ44 UniProt - Putative antiporter subunit mnhD2 | |||
*#SAR1409 - Q6GH11 UniProt - Catalyzes the transfer of an acetyl group from acetyl-CoA to tetrahydrodipicolinate. INCREASED | |||
*#SAR2697 - Q6GDI4 UniProt - No other info INCREASED | |||
*#SAR2146 - Q6GF14 UniProt - Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate INCREASED | |||
*#SAR0689 - pseudogene | |||
*#SAR2771 - hypothetical protein | |||
*#SAR0278 - hypothetical protein | |||
*#SAR1563 - pseudogene | |||
*#SAR0820 - Q6GIM6 UniProt - Displays ATPase and GTPase activities. INCREASED | |||
*#SAR0353 - Q6GJW2 UniProt - Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. INSCREASED | |||
*This is a file that zeb put together. It deals with all the decreasing and increasing GO terms along with their screenshots. [[Media:ZR_MRSA.zip | gene MRSA screenshots etc.]] | |||
*Working on the powerpoint and so far it can be found [[Media:FinalPowerpointACnew.ppt | here]]. | |||
*The final powerpoint presentation can be found [[Media:FinalPowerpointACnew.ppt | here]]. | |||
==Links== | |||
*[[User:Alex A. Cardenas|Alex A. Cardenas]] | |||
*[[BIOL368/F11:Week 14|Week 14 Assignment]] | |||
*[[Alex A. Cardenas Week 2]] | |||
*[[Alex A. Cardenas Week 3]] | |||
*[[Alex A. Cardenas Week 4]] | |||
*[[Alex A. Cardenas Week 5]] | |||
*[[Alex A. Cardenas Week 6]] | |||
*[[Alex A. Cardenas Week 7]] | |||
*[[Alex A. Cardenas Week 8]] | |||
*[[Alex A. Cardenas Week 9]] | |||
*[[Alex A. Cardenas Week 10]] | |||
*[[Alex A. Cardenas Week 11]] | |||
*[[Alex A. Cardenas Week 12]] | |||
*[[Alex A. Cardenas Week 14]] | |||
*[[BIOL368/F11:Class Journal Week 1|Class Journal Week 1]] | |||
*[[BIOL368/F11:Class Journal Week 2|Class Journal Week 2]] | |||
*[[BIOL368/F11:Class Journal Week 3|Class Journal Week 3]] | |||
*[[BIOL368/F11:Class Journal Week 5|Class Journal Week 5]] | |||
*[[BIOL368/F11:Class Journal Week 6|Class Journal Week 6]] | |||
*[[BIOL368/F11:Class Journal Week 7|Class Journal Week 7]] | |||
*[[BIOL368/F11:Class Journal Week 8|Class Journal Week 8]] | |||
*[[BIOL368/F11:Class Journal Week 9|Class Journal Week 9]] | |||
*[[BIOL368/F11:Class Journal Week 10|Class Journal Week 10]] | |||
*[[BIOL368/F11:Class Journal Week 11|Class Journal Week 11]] | |||
*[[BIOL368/F11:Class Journal Week 12|Class Journal Week 12]] | |||
*[[BIOL368/F11:Class Journal Week 14|Class Journal Week 14]] | |||
[[Category:BIOL368/F11]] |
Latest revision as of 23:33, 6 December 2011
Electronic Notebook
- Computed the averages for A,B, and C along with multiplying all the c3/c5 by negative 1.
- Worked through the protocall and computed the Tstat values and the Pvalues along with changing some of the columns and rows.
- Filtered out the Pvalue column to find how many genes Pvalues were less than 0.05, 0.01, and 0.001.
- Pvalue < 0.05 - 680 genes.
- Pvalue < 0.01 - 228 genes.
- Pvalue < 0.001 - 26 genes.
- The new spreadsheet can be found here.
- More modified spreadsheet can be found here.
- When making the geneMAPP, there were 132 errors found but this is insignificant because this is out of 2740 genes.
- geneMAPP excel file can be found here. The text file for geneMAPP can be found here.
- We looked at the top 10 genes with the lowest Pvalues, and the excel file can be found here.
- We also looked at the top 10 Gene Ontology terms and those can be found below.
- Pathogenesis
- Multi-organism process
- External encapsulating structure
- High-affinity iron ion transport
- Extracellular region
- Membrane Part
- Protein complex binding
- Immunoglobin binding
- Respiratory chain
- Periplasmic space
- Top ten increasing GO terms looked at will be:
- amine biosynthetic process
- cellular amino acid biosynthetic process
- cellular nitrogen compound biosynthetic process
- antiport activity
- branched chain family amino acid metabolic process
- aspartate family amino acid metabolic process
- threonine metabolic process
- oxidation reduction
- vitamin binding
- oxidoreductace activity
- Most Significant Genes
- SAR0633 - Q6GJ44 UniProt - Putative antiporter subunit mnhD2
- SAR1409 - Q6GH11 UniProt - Catalyzes the transfer of an acetyl group from acetyl-CoA to tetrahydrodipicolinate. INCREASED
- SAR2697 - Q6GDI4 UniProt - No other info INCREASED
- SAR2146 - Q6GF14 UniProt - Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate INCREASED
- SAR0689 - pseudogene
- SAR2771 - hypothetical protein
- SAR0278 - hypothetical protein
- SAR1563 - pseudogene
- SAR0820 - Q6GIM6 UniProt - Displays ATPase and GTPase activities. INCREASED
- SAR0353 - Q6GJW2 UniProt - Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. INSCREASED
- This is a file that zeb put together. It deals with all the decreasing and increasing GO terms along with their screenshots. gene MRSA screenshots etc.
- Working on the powerpoint and so far it can be found here.
- The final powerpoint presentation can be found here.
Links
- Alex A. Cardenas
- Week 14 Assignment
- Alex A. Cardenas Week 2
- Alex A. Cardenas Week 3
- Alex A. Cardenas Week 4
- Alex A. Cardenas Week 5
- Alex A. Cardenas Week 6
- Alex A. Cardenas Week 7
- Alex A. Cardenas Week 8
- Alex A. Cardenas Week 9
- Alex A. Cardenas Week 10
- Alex A. Cardenas Week 11
- Alex A. Cardenas Week 12
- Alex A. Cardenas Week 14
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 7
- Class Journal Week 8
- Class Journal Week 9
- Class Journal Week 10
- Class Journal Week 11
- Class Journal Week 12
- Class Journal Week 14