J'aime C. Moehlman's Week 13: Difference between revisions
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===MAPPFinder Criterion=== | ===MAPPFinder Criterion=== | ||
*[[Media:Vc MAPPFinder Results 3-Criterion0-GO.xls|Increased]] | *[[Media:Vc MAPPFinder Results 3-Criterion0-GO.xls|Increased]] | ||
*|Decreased]] | *[[Media:Vc MAPPFinder Results 3-Criterion1-GO.xls|Decreased]] | ||
Revision as of 11:30, 20 April 2010
GenMAPP Expression Dataset Manager Procedure
- There were 772 errors detected in the raw data for V. cholerae, thus they were not not converted.
- We then created a color sets based off of set criteria.
- We uploaded it onto lionshare in order to save it.
- Ran the MAPPFinder for our two criteria; criteria one is based on the average FC of all being greater than .25 and pvalue is less than .05. Criteria 2 says the average is less than -.25 and less than .05.
- top 10 gene ontology:
- protein folding
- unfolded protein binding
- cytoplasm
- cis-trans isomerase activity
- peptidyl-prolyl-cis-trans isomerase activity
- chorismate metabolic process
- aromatic amino acid family biosynthetic process
- protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
- phosphoenolpyruvate-dependent sugar phosphotransferase system
- intracellular part
- there is an increase in expression, and also a decrease in expression; finding the GO terms associated with both inc. and dec.; they each have a process(ex: glycolysis), component(location in cell), and function(type of enzyme)
EX: (increased) glycolysis has 10 enzymes, 10 genes.
- what processes are involved in making vc pathogenic?
filtering: pvalue z score number changed percent changed www. geneontology. org-- definitions.
specific GO terms for Genes mentioned by Merrell
- VC0028- not found
- VC0941- not found
- VC0869- not found
- VC0051- not found
- VC0647- biological processes- mRNA catabolic processes, bilogical processes- 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- establishment of localization- transport, cellular component- envelope (cell envelope) outermembrane bounded periplasmic space, molecular function- transport activity
- Clicked on mRNA catabolic process for Gene VC0647- and it showed genes: 1 (PNP_VIBCH) showed decreased expression and the other (CSRA_VIBCH) showed no change.
- The mRNA catabolic process backpage shows that the function mRNA breakdown or catabolism. This is the chemical reactions and pathways resulting in the breakdown of mRNA.
MAPPFinder Criterion
