Chris Rhodes Week 14: Difference between revisions
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#aldehyde dehydrogenase [NAD(P)+] activity: Catalysis of the reaction: an aldehyde + NAD(P)+ + H2O = an acid + NAD(P)H + H+ [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0004030&session_id=7048amigo1323123541 AmiGO Link] | #aldehyde dehydrogenase [NAD(P)+] activity: Catalysis of the reaction: an aldehyde + NAD(P)+ + H2O = an acid + NAD(P)H + H+ [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0004030&session_id=7048amigo1323123541 AmiGO Link] | ||
#oxidoreductase activity:The catalysis of redox reactions specifically relating to energy functions such as NAD+/NADH [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0016491&session_id=6850amigo1323121684 AmiGO Link] | #oxidoreductase activity:The catalysis of redox reactions specifically relating to energy functions such as NAD+/NADH [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0016491&session_id=6850amigo1323121684 AmiGO Link] | ||
#inositol | #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 [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0052745&session_id=1133amigo1323123692 AmiGO Link] | ||
#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 [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006081 AmiGO Link] | #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 [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006081 AmiGO Link] | ||
Revision as of 19:43, 5 December 2011
Files
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
Using the updated data spread sheet from the Week 13 Journal
Decreased GO Terms
- fructuronate reductase activity: Catalysis of the reaction: D-mannonate + NAD(+) = D-fructuronate + H(+) + NADH AmiGO Link
- precorrin-3B C17-methyltransferase activity: Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-3B = S-adenosyl-L-homocysteine + precorrin AmiGO Link
- precorrin-2 C20-methyltransferase activity:Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-2 = S-adenosyl-L-homocysteine + H(+) + precorrin-3A AmiGO Link
- coniferyl-aldehyde dehydrogenase activity: Catalysis of the reaction: coniferyl aldehyde + H2O + NAD(P)+ = ferulate + NAD(P)H + H+ AmiGO Link
- inositol-1(or 4)-monophosphatase activity: Catalysis of the reaction: myo-inositol phosphate + H2O = myo-inositol + phosphate AmiGO Link
- trans-2-enoyl-CoA reductase (NADPH) activity: Catalysis of the reaction: acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH + H+ AmiGO Link
- aldehyde dehydrogenase [NAD(P)+] activity: Catalysis of the reaction: an aldehyde + NAD(P)+ + H2O = an acid + NAD(P)H + H+ AmiGO Link
- oxidoreductase activity:The catalysis of redox reactions specifically relating to energy functions such as NAD+/NADH AmiGO Link
- 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
- 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
- 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
- regulation of transcription: Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription AmiGO Link
- 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
- 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
- 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
- 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
- regulation of cellular macromolecule biosynthetic process: Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process AmiGO Link
- 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
- 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
- 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
- MSMEG_0410: MmpL Protein, 0.001619392
- MSMEG_0471: Transcriptional Regulator LysR Family Protein, 0.000589115
- MSMEG_1127: Probable Conserved Transmembrane Protein, 0.001345606
- MSMEG_1161: Taurine Transport System Permease Protein TauC, 0.002122214
- MSMEG_2951: [2Fe-2S] Binding Domain Protein, 0.002674215
- MSMEG_3446: Hypothetical Protein, 0.002569072
- MSMEG_4511: Linear Gramicidin Synthetase mbtf, 0.00059067
- MSMEG_4525: Putative Oxygen-Independent Coproporhyrinogen III Oxidase, 0.003370748
- MSMEG_6415: Conserved Hypothetical Protein, 0.003256267
- 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
Links
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