Difference between revisions of "Kevinmcgee Week 15"
From LMU BioDB 2013
Kevinmcgee (Talk | contribs) (Added Sanity Check) |
Kevinmcgee (Talk | contribs) (→Running MAPPFinder) |
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| − | =Sanity Check= | + | =Uploading Into GenMAPP= |
| − | ==Leishmania Infantum== | + | ==Datasheet== |
| + | #compiled all data onto a single data sheet including both L.Major and L.Infantum and uploaded into GenMAPP | ||
| + | #*Ran into some problems uploading (almost everything was an error) | ||
| + | #Filtered out any Lin genes and created a new datasheet for only LmfJ genes. | ||
| + | #*Still ran into problems uploading | ||
| + | #looked at the database OrthologicalNames sheet, and saw that the GeneID's were in a different format on there then in the spreadsheet. | ||
| + | #*Made a quick-fix file by changing the names on the spreadsheet, but longterm fixes are being made to the coding so that other users do not have to change the names on their spreadsheets every time (for convenience). | ||
| + | #Were able to upload our data and continue on with the project. | ||
| + | ==Sanity Check== | ||
| + | ===Leishmania Infantum=== | ||
#Filtered P-value | #Filtered P-value | ||
| − | #* | + | #*1392 genes were <.05 |
| − | #* | + | #*327 genes were <.01 |
| − | #* | + | #*67 genes were <.001 |
| − | #* | + | #*28 genes were >.0001 |
#Filtered Average Log Fold Change | #Filtered Average Log Fold Change | ||
| − | #* | + | #*748 genes were >0 |
| − | #* | + | #*646 genes were <0 |
| − | #* | + | #*699 genes were >.25 while 646 were <.05 |
| − | #* | + | #*748 genes were >.05 while 606 were <.-25 |
| + | ==MAPPFinder Color Changes== | ||
| + | #The colors were assigned to the two main criterion | ||
| + | #*Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored blue | ||
| + | #*Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored purple | ||
| + | ==Running MAPPFinder== | ||
| + | *Set up MAPPFinder to run with the file name LMajorGOMap | ||
| + | *Ran for about 1 1/2 hours | ||
| + | #Top Ten GO Terms | ||
| + | #*catalytic activity | ||
| + | #*Endonuclease activity | ||
| + | #*DNA catabolic process | ||
| + | #*Aromatic compound catabolic process | ||
| + | #*cellular nitrogen compound catabolic process | ||
| + | #*nucleobase-containing compound catabolic process | ||
| + | #*organic cyclic compound catabolic process | ||
| + | #*heterocycle catabolic process | ||
| + | #*oxidoreductase activity | ||
| + | #*macromolecular complex | ||
| + | |||
| + | |||
| + | [[image: Picture GO.PNG]] | ||
Latest revision as of 01:01, 8 December 2013
Contents |
[edit] Uploading Into GenMAPP
[edit] Datasheet
- compiled all data onto a single data sheet including both L.Major and L.Infantum and uploaded into GenMAPP
- Ran into some problems uploading (almost everything was an error)
- Filtered out any Lin genes and created a new datasheet for only LmfJ genes.
- Still ran into problems uploading
- looked at the database OrthologicalNames sheet, and saw that the GeneID's were in a different format on there then in the spreadsheet.
- Made a quick-fix file by changing the names on the spreadsheet, but longterm fixes are being made to the coding so that other users do not have to change the names on their spreadsheets every time (for convenience).
- Were able to upload our data and continue on with the project.
[edit] Sanity Check
[edit] Leishmania Infantum
- Filtered P-value
- 1392 genes were <.05
- 327 genes were <.01
- 67 genes were <.001
- 28 genes were >.0001
- Filtered Average Log Fold Change
- 748 genes were >0
- 646 genes were <0
- 699 genes were >.25 while 646 were <.05
- 748 genes were >.05 while 606 were <.-25
[edit] MAPPFinder Color Changes
- The colors were assigned to the two main criterion
- Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored blue
- Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored purple
[edit] Running MAPPFinder
- Set up MAPPFinder to run with the file name LMajorGOMap
- Ran for about 1 1/2 hours
- Top Ten GO Terms
- catalytic activity
- Endonuclease activity
- DNA catabolic process
- Aromatic compound catabolic process
- cellular nitrogen compound catabolic process
- nucleobase-containing compound catabolic process
- organic cyclic compound catabolic process
- heterocycle catabolic process
- oxidoreductase activity
- macromolecular complex
