Chris Rhodes Week 14

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(Methods)
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*How do your results and hypothesis align with the paper you read?
*How do your results and hypothesis align with the paper you read?
==Methods==
==Methods==
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Using the updated data spread sheet from the Week 13 Journal
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All important files used in this weeks experiment can be found in the Files section above.
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Using the [[Media:Nicolette_Chris_ MasterSpreadSheet_20111130.xls| updated data spread sheet]] from the Week 12 Journal we used excell to calculate the average log<sub>2</sub> value, the p-values, and the tstat values for each experiment, fast/slow,2.5%/50%, and 0.6%/50%.
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*Average= AVERAGE(A2:E2)
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*TStat= AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(number of replicates)) where number of replicates=5
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*P-value=TDIST(ABS(R2),degrees of freedom,2) where degrees of freedom=(5-1)=4
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Using the filter function in excel, the experiment with the largest amount of significant genes (p<0.05) was found. This was the 2.5%/50% experiment with a total of 215 significant genes. This was a relatively small number considering the total number of genes studied was 6947. Using another filter function the top ten most significant genes were found in the 2.5%/50% experiment data. These genes, their p values, and their functions are listed below. The data from the 2.5/50 experiment was compiled and run through MAPPFinder in order to find increased and decreased ontologies in the experiment. MAPPFinder produced 2 txt files 1 for increased ontologies and another for decreased ontologies. By uploading these txt files into excel and using a filter function, the top ten most significantly increased and decreased ontologies were found. These ontologies and a description of their functions can be found below.
==Decreased GO Terms==
==Decreased GO Terms==

Revision as of 00:57, 7 December 2011

Contents

Files

Calculations XLS

GenMapp TXT

Increased MAPPFinder Results XLS

Decreased MAPPFinder Results XLS

Increased MAPPFinder Results TXT

Decreased MAPPFinder Results TXT

Materials we need

  • Table of significant genes at p< 0.05,0.01,0.001
  • Top ten significant genes
  • Top ten increased/decreased GO terms
  • Make a list of the functions of the top ten genes.
  • Take all of this data and hypothesize why under the conditions of the experiment they would be up or down regulated.
  • How do your top ten significant genes relate to the GO terms? How do they relate to the experimental conditions?
  • How do your results and hypothesis align with the paper you read?

Methods

All important files used in this weeks experiment can be found in the Files section above. Using the updated data spread sheet from the Week 12 Journal we used excell to calculate the average log2 value, the p-values, and the tstat values for each experiment, fast/slow,2.5%/50%, and 0.6%/50%.

  • Average= AVERAGE(A2:E2)
  • TStat= AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(number of replicates)) where number of replicates=5
  • P-value=TDIST(ABS(R2),degrees of freedom,2) where degrees of freedom=(5-1)=4

Using the filter function in excel, the experiment with the largest amount of significant genes (p<0.05) was found. This was the 2.5%/50% experiment with a total of 215 significant genes. This was a relatively small number considering the total number of genes studied was 6947. Using another filter function the top ten most significant genes were found in the 2.5%/50% experiment data. These genes, their p values, and their functions are listed below. The data from the 2.5/50 experiment was compiled and run through MAPPFinder in order to find increased and decreased ontologies in the experiment. MAPPFinder produced 2 txt files 1 for increased ontologies and another for decreased ontologies. By uploading these txt files into excel and using a filter function, the top ten most significantly increased and decreased ontologies were found. These ontologies and a description of their functions can be found below.

Decreased GO Terms

  1. fructuronate reductase activity: Catalysis of the reaction: D-mannonate + NAD(+) = D-fructuronate + H(+) + NADH AmiGO Link
  2. precorrin-3B C17-methyltransferase activity: Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-3B = S-adenosyl-L-homocysteine + precorrin AmiGO Link
  3. precorrin-2 C20-methyltransferase activity:Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-2 = S-adenosyl-L-homocysteine + H(+) + precorrin-3A AmiGO Link
  4. coniferyl-aldehyde dehydrogenase activity: Catalysis of the reaction: coniferyl aldehyde + H2O + NAD(P)+ = ferulate + NAD(P)H + H+ AmiGO Link
  5. inositol-1(or 4)-monophosphatase activity: Catalysis of the reaction: myo-inositol phosphate + H2O = myo-inositol + phosphate AmiGO Link
  6. trans-2-enoyl-CoA reductase (NADPH) activity: Catalysis of the reaction: acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH + H+ AmiGO Link
  7. aldehyde dehydrogenase [NAD(P)+] activity: Catalysis of the reaction: an aldehyde + NAD(P)+ + H2O = an acid + NAD(P)H + H+ AmiGO Link
  8. oxidoreductase activity:The catalysis of redox reactions specifically relating to energy functions such as NAD+/NADH AmiGO Link
  9. inositol phosphatase activity: Catalysis of the reaction: inositol phosphate(n) + H2O = inositol phosphate(n-1) + phosphate. This reaction is the removal of a phosphate group from an inositol phosphate AmiGO Link
  10. cellular aldehyde metabolic process: The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells AmiGO Link

Increased GO Terms

  1. RNA metabolic process: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage AmiGO Link
  2. regulation of transcription: Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription AmiGO Link
  3. regulation of nitrogen compound metabolic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds AmiGO Link
  4. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process: Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids AmiGO Link
  5. regulation of macromolecule biosynthetic process: Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule. AmiGO Link
  6. regulation of gene expression: Any process that modulates the frequency, rate or extent of gene expression. This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein AmiGO Link
  7. regulation of cellular macromolecule biosynthetic process: Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process AmiGO Link
  8. regulation of cellular biosynthetic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells AmiGO Link
  9. regulation of biosynthetic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances AmiGO Link
  10. regulation of macromolecule metabolic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules.AmiGO Link

Top Ten Regulated Genes

ID Number: Protein Name, p-value

  1. MSMEG_0410: MmpL Protein, 0.001619392
  2. MSMEG_0471: Transcriptional Regulator LysR Family Protein, 0.000589115
  3. MSMEG_1127: Probable Conserved Transmembrane Protein, 0.001345606
  4. MSMEG_1161: Taurine Transport System Permease Protein TauC, 0.002122214
  5. MSMEG_2951: [2Fe-2S] Binding Domain Protein, 0.002674215
  6. MSMEG_3446: Hypothetical Protein, 0.002569072
  7. MSMEG_4511: Linear Gramicidin Synthetase mbtf, 0.00059067
  8. MSMEG_4525: Putative Oxygen-Independent Coproporhyrinogen III Oxidase, 0.003370748
  9. MSMEG_6415: Conserved Hypothetical Protein, 0.003256267
  10. MSMEG_6852: Putative Carboxylesterase/Lipase, 0.000659307

Table of Significant Genes

Showing the number of genes with a p value below certain thresholds in the 50%/2.5% Oxygen Limited Experiment

p<     Number of Genes    
0.05         215
0.01         42
0.001        3

Discussion

Presentation

Final Presentation

Links

  1. Chris Rhodes User Page
  2. Week 2 Journal
  3. Week 3 Journal
  4. Week 4 Journal
  5. Week 5 Journal
  6. Week 6 Journal
  7. Week 7 Journal
  8. Week 8 Journal
  9. Week 9 Journal
  10. Week 10 Journal
  11. Week 11 Journal
  12. Week 12 Journal
  13. Week 13 Journal
  14. Week 14 Journal
  15. Home Page
  16. Week 5 Assignment Page
  17. Week 6 Assignment Page
  18. Week 7 Assignment Page
  19. Week 8 Assignment Page
  20. Week 9 Assignment Page
  21. Week 10 Assignment Page
  22. Week 11 Assignment Page
  23. Week 12 Assignment Page
  24. Week 13 Assignment Page
  25. Week 14 Assignment Page
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