Difference between revisions of "Malverso Week 8"

Revision as of 20:29, 25 October 2015

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File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).xls

File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).txt

File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).gex

File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).EX.txt

Sanity Check: Number of Genes Significantly Changed

• Number of genes with a p value less than .05 = 948. This is 18.16% of the genes.
• Number of genes with a p value less than .01 = 235. This is 4.50% of the genes.
• Number of genes with a p value less than .001 = 24. This is 0.46% of the genes.
• Number of genes with a p value less than .0001 = 2. This is 0.04% of the genes.
• Number of genes with a Bonferroni p value less than .05 = 0. This is 0% of the genes.
• Number of genes with a B-H p value less than .05 = 0. This is 0% of the genes.
• Avg_LogFC_all > 0 = 352. 6.7%
• < 0 = 596. 11.34%
• > .25 = 339. 17.83%
• <-.25 = 579. 11.09%
• "two-class SAM analysis was conducted" "with statistically significant changes in the level of expression - at least a twofold change" They used the actual level of expression change to figure out what was significant while we used p value (which is the probability that changes in expression are due to chance). Merrell et al. (2002) used a more stringent method because they found 237 genes that were significantly changed while we found 918. (-.25 < pvalue > .25)

Sanity Check: Compare Individual Genes with Known Data

• VC0028 fold change: 1.65 pvalue:.0474 and 1.27 .0692
• first is sig changed, second is not
• VC0941 -.28 .1636 and .88 .0001
• VC0869 Fold changes: 2.12, 1.50, 1.59, 1.95, 2.20

P value: 0.02, 0.0174, 0.0463, 0.0227, 0.002 All are significantly changed

• VC0051 Fold change: 1.89, 1.92

P value: 0.016, 0.0139 Both are significantly changed

• VC0647 fold change: -1.11 pvalue:.0003 and fold change:-0.94 pvalue:.0125 and fold change:-1.05 pvalue:.0051
• VC0468 -.17 and pvalue:.3350
• VC2350 fold change: -2.40 pvalue:.0130
• VCA0583 fold change: 1.06 pvalue: .1011

Part Two

• I used the 2010 database.
• There were 121 errors.
• Kristin used the 2009 database and 772 errors were detected.
• My database is newer and therefore it makes sense that the number of errors has decreased from the previous year, because it makes sense that the change in the database from 2009 - 2010 was an improvement. The database I used probably has more entries and less bugs.
• We were an increased pair, which I labeled red.
• I labeled decreased with green.

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 biosynthetic process
6. purine ribonucleoside monophosphate metabolic process
7. purine nucleoside monophosphate metabolic process
8. purine nucleoside monophosphate biosynthetic process
9. 'de novo' IMP biosynthetic process
10. arginine metabolic process

• Our results were completely different. There must have been some significant findings in the year 2009 that uncovered significant gene changes.

Team Page

Heavy Metal HaterZ

Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 13
• Week 14
• Week 15

Individual Journal Entries

• Malverso User Page (Week 1)
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 13
• Week 14
• Week 15

Shared Journal Entries

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 13
• Week 14
• Week 15