Difference between revisions of "Eyanosch Week 15"
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==Electronic lab notebook== | ==Electronic lab notebook== | ||
| − | * | + | *Ran GenMAPP and produced Criterion0-GO.txt files for increased and decreased of both RP drug times. with the data from the GO map. Analyzed this data in excel |
| − | * | + | *Opened 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) | *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) | *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 | *Something interesting to note is that Cell Projection had 35/42 | ||
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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. | 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. | ||
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=====Increased===== | =====Increased===== | ||
| + | |||
| + | The genes that showed an increase in expression were mainly associated with flagellar assembly and motility. I.E. cell projection, pilus, cell adhesion, bacterial-type flagellum, etc. | ||
=====Decreased===== | =====Decreased===== | ||
| + | |||
| + | The genes that showed a decrease in expression were associated with ribosomes and protein synthesis. I.E. translation, peptide biosynthetic process, peptide metabolic process, ribosome, RNA binding, etc. | ||
===RP-0.5-10 Increased and Decreased=== | ===RP-0.5-10 Increased and Decreased=== | ||
=====Increased===== | =====Increased===== | ||
| + | |||
| + | The genes that showed an increase in expression were involved in metabolic processes and cell projection. I.E. NADP metabolic process, glucose 6-phosphate metabolic process, nucleoside phosphate metabolic process, cellular metabolic compound salvage, cell projection organization, etc. | ||
=====Decreased===== | =====Decreased===== | ||
| − | + | The genes that showed a decease in expression were involved in the ribosome. I.E. Ribosome, ribonucleoprotein complex, structural constituent of ribosome, structural molecule activity, translation, etc. | |
| + | |||
| + | =====Flagellar assembly===== | ||
| + | *Looked 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 | ||
| + | *If the box appears blank, just reset the desired expression data set. | ||
| + | |||
| + | =====Ribosome===== | ||
| + | *Searched genes related to Ribosome - Shigella flexneri 301 (serotype 2a) | ||
| + | *Completed same process as denoted within Flagellar assembly | ||
| + | |||
| + | =====Metabolic Process===== | ||
| + | *Searched genes related to the metabolic processes of Glycolysis and the TCA cycle | ||
| + | *Completed same process as Flagellar assembly | ||
| + | |||
| + | ====Create Genes on our Map==== | ||
| + | *searched genes based on the pathways of greatest expression | ||
| + | *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) | ||
| + | |||
| + | ===PowerPoint=== | ||
| + | *worked on slides | ||
| + | **Background for Shigella flexneri | ||
| + | **GenMAPP MAPP slides and the pathways involved | ||
| + | **Overall final analysis part | ||
| + | [[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']] | ||
All the current files are located under RP (Erich) of the [[OTS Files | Wiki page]] | All the current files are located under RP (Erich) of the [[OTS Files | Wiki page]] | ||
Latest revision as of 07:33, 15 December 2015
Contents
Erich Yanoschik
Electronic lab notebook
- Ran GenMAPP and produced Criterion0-GO.txt files for increased and decreased of both RP drug times. with the data from the GO map. Analyzed this data in excel
- Opened 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
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
The genes that showed an increase in expression were mainly associated with flagellar assembly and motility. I.E. cell projection, pilus, cell adhesion, bacterial-type flagellum, etc.
Decreased
The genes that showed a decrease in expression were associated with ribosomes and protein synthesis. I.E. translation, peptide biosynthetic process, peptide metabolic process, ribosome, RNA binding, etc.
RP-0.5-10 Increased and Decreased
Increased
The genes that showed an increase in expression were involved in metabolic processes and cell projection. I.E. NADP metabolic process, glucose 6-phosphate metabolic process, nucleoside phosphate metabolic process, cellular metabolic compound salvage, cell projection organization, etc.
Decreased
The genes that showed a decease in expression were involved in the ribosome. I.E. Ribosome, ribonucleoprotein complex, structural constituent of ribosome, structural molecule activity, translation, etc.
Flagellar assembly
- Looked 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.
Ribosome
- Searched genes related to Ribosome - Shigella flexneri 301 (serotype 2a)
- Completed same process as denoted within Flagellar assembly
Metabolic Process
- Searched genes related to the metabolic processes of Glycolysis and the TCA cycle
- Completed same process as Flagellar assembly
Create Genes on our Map
- searched genes based on the pathways of greatest expression
- 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)
PowerPoint
- worked on slides
- Background for Shigella flexneri
- GenMAPP MAPP slides and the pathways involved
- Overall final analysis part
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
