Difference between revisions of "Eyanosch Week 15"
From LMU BioDB 2015
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Revision as of 21:36, 12 December 2015
Contents
Erich Yanoschik
Electronic lab notebook
- When GenMAPP is run it creates a Criterion0-GO.txt file with the data from the GO map. Analyze this data in excel
- Open the Criterion0-GO.txt file in excel
- Focus on the most Induced or Repressed GO terms so set the Z score Greater than 2, PermuteP less than 0.05, Adjusted P less than 0.1, and Number Changed (is greater than or equal to 4, and is less than or equal to 100)
- For RP-1-60 The major Genes Induced dealt with cell motility (Cell projection, pilus, cell adhesion, and biological adhesion)
- Something interesting to note is that Cell Projection had 35/42
Create Genes on our Map
- to create genes on our map click the gene button on the left next to label, click a place on the map.
- Go to http://www.genome.jp/kegg/pathway.html (Kegg pathway Database)
- search organism Shigella Flexneri 301 (serotype 2a)
- Enter the GO keyword or pathway you are looking into (I.E. cell projection)
Flagellar assembly
- Looking up genes for Flagellar assembly - Shigella flexneri 301 (serotype 2a) at (http://www.genome.jp/kegg-bin/show_pathway?org_name=sfl&mapno=02040&mapscale=&show_description=show)
- right click on the gene box and enter the information for Gene identification
- Gene ID
- SF1966
- Gene ID System
- OrderedLocusNames
- Gene Label
- fliC
- Gene ID
- If the box appears blank, just reset the desired expression data set.
I will be working on the RPs and Kristin will be working on the RXs of the same time points and compare our results. (We hypothesize that we will see similar Inductions and Reductions of Genes.
RP-1-60 Increased and Decreased
Increased
Decreased
RP-0.5-10 Increased and Decreased
Increased
Decreased
Created map for ribosomal related genes
All the current files are located under RP (Erich) of the Wiki page
Class Journals
Weekly Assignments
Personal Journal
Eyanosch Week 15
Electronic Notes (E-notes)
Class (personal) Notes
