Amanda N. Wavrin Week 13

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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


Presentation

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Useful Links

Weekly Journals


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