Difference between revisions of "Alex A. Cardenas Week 14"
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This is 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.]]
Revision as of 16:51, 6 December 2011
- 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.
- 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.
- 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