Amanda N. Wavrin Week 13: Difference between revisions

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===Top 10 GO terms for criterion 0===
#Macromolecule metabolic process
#Cellular biopolymer biosynthetic process
#Biopolymer biosynthetic process
#Cellular macromolecule biosynthetic process
#Macromolecule biosynthetic process
#Biopolymer metabolic process
#Cellular macromolecule metabolic process
#Purine base metabolic process
#Purine base biosynthetic process
#Cell projection organization


 
===Top 10 GO terms for criterion 1===
 
#'''Protein folding'''
#Chorismate metabolic process
#Aromatic amino acid family biosynthetic process
#Unfolded protein folding
#Cytoplasm
#Zinc ion binding
#'''Intracellular part'''
#Protein-N(PI)-phosphohistidine-sugar phosphotranferase activity
#Sugar:hydrogen symporter activity
#Cation:sugar symporter activity




Revision as of 21:07, 25 April 2010

GenMAPP and MAPPfinder

  • Changed the gene database to the V. cholerae database
  • Expression Dataset Manager converted our data
  • There were 772 errors
  • Customized the new Expression Dataset by creating new Color Sets
  • Saved the .gex file to lionshare
  • Saved the MAPPFinder results to the desktop and ran MAPPFinder
  • Top 10 Gene Ontology terms for criteria 1-Deacreased:
  1. Protein folding
  2. Unfolded protein binding
  3. Cytoplasm
  4. Cis-trans isomerase activity
  5. Peptidyl-prolyl-cid-trans isomerase activity
  6. Chorismate metabolic process
  7. Aromatic amino acid family biosynthetic process
  8. Protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
  9. Phosph0enolpyruvate-dependent sugar phosphotransferase system
  10. Intracellular part
  • Searched the MAPPFinder browser for specific genes to find GO terms associated with each:
    • VC0028: Not found
    • VC0941: Not found
    • VC0869: Not found
    • VC0051: Not found
    • VC0647: Biological process- mRNA catabloic process, biological process- RNA processing, cellular component- cytoplasm, molecular function- RNA binding, catalytic activity- 3'-5' exoribonuclease activity,catalytic activity- transferase activity, catalytic activity-nucleotidyltransferase activity, catalytic activity- polyribonucleotide nucleotidyltransferase activity
    • VC0468: Not found
    • VC2350: Not found
    • VCA0583: Biological process- transport, cellular component- envelope (cell envelope) outer membrane-bound periplasmic space, molecular function- transporter activity
  • Clicked on mRNA catabolic process from Gene VC0647 to get all fo the genes associated with this term. Gene CSRA_VIBCH showed no significant change. Gene PNP_VIBCH showed decreased expression.
  • Uploaded this MAPP to my lionshare
    • The function of this gene is mRNA breakdown or catabolism. This is the chemical reactions and pathways resulting in the breakdwon of mRNA.
  • Autofiltered the spreadsheets for increasing and decreasing expression and uploaded them

MAPPFinder criterion



Top 10 GO terms for criterion 0

  1. Macromolecule metabolic process
  2. Cellular biopolymer biosynthetic process
  3. Biopolymer biosynthetic process
  4. Cellular macromolecule biosynthetic process
  5. Macromolecule biosynthetic process
  6. Biopolymer metabolic process
  7. Cellular macromolecule metabolic process
  8. Purine base metabolic process
  9. Purine base biosynthetic process
  10. Cell projection organization

Top 10 GO terms for criterion 1

  1. Protein folding
  2. Chorismate metabolic process
  3. Aromatic amino acid family biosynthetic process
  4. Unfolded protein folding
  5. Cytoplasm
  6. Zinc ion binding
  7. Intracellular part
  8. Protein-N(PI)-phosphohistidine-sugar phosphotranferase activity
  9. Sugar:hydrogen symporter activity
  10. Cation:sugar symporter activity





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