Amanda N. Wavrin Week 13

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

 * [[Media:Vc MAPPFinder Results 3-Criterion0-GO.xls|Increased]]
 * [[Media:Vc MAPPFinder Results 3-Criterion1-GO.xls|Decreased]]

Presentation
[[Media:Bioinformatics Microarray Data Project.ppt|Powerpoint]]

[[Media:Bioinformatics Microarray Data Project FINAL.ppt|New Powerpoint]]