Difference between revisions of "Heavy Metal HaterZ Files"
From LMU BioDB 2015
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*Appropriate way to title files: | *Appropriate way to title files: | ||
**FileName_YYYYMMDD_HMH | **FileName_YYYYMMDD_HMH | ||
| + | |||
| + | ===Gene Database=== | ||
| + | *[[File:So-Std_HMH_20151214.zip]] | ||
| + | |||
===Initial Flow Chart=== | ===Initial Flow Chart=== | ||
| Line 16: | Line 20: | ||
===GenMapp Builder=== | ===GenMapp Builder=== | ||
| + | *Note:This is now outdated. | ||
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]] | *[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]] | ||
| Line 39: | Line 44: | ||
===MAPPFinder Documents=== | ===MAPPFinder Documents=== | ||
| + | *gdb file - [[File:So-Std 20151201special.zip]] | ||
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]] | *[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]] | ||
| − | *Filtered GO terms - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]] | + | *GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]] |
| + | *Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]] | ||
| + | **[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]] | ||
| + | *Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]] | ||
| + | **[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]] | ||
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]] | *Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]] | ||
| + | *MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]] | ||
| + | **Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]] | ||
| + | *MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]] | ||
| + | **Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]] | ||
| + | *MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]] | ||
| + | **Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]] | ||
| + | *MAPP for Compiled Fatty Acid Degradation -[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp]] | ||
| + | **Screenshot of results - [[File:Fatty Acid Degradation Compiled 20151216 HMH.PNG]] | ||
| + | |||
| + | ===KEGG Screenshots=== | ||
| + | *Fatty Acid Degradation [[File:Fatty Acid Pathway from KEGG 20151216 HMH.PNG]] | ||
| + | *Ribosome [[File:Ribosome Pathway from KEGG 20151216 HMH.PNG]] | ||
| + | |||
| + | ===Tables for Paper=== | ||
| + | *Table showing variations between Yang et al. paper for 6 chosen genes and our results - [[File:Gene Comparison 20151216 HMH.xlsx]] | ||
| + | *Tale showing variations between Yang et al. paper for genes involved in the ribosome pathway and our results - [[File:Ribosome Pathway Comparison 20151216 HMH.xlsx]] | ||
[[Category:Heavy Metal HaterZ]] | [[Category:Heavy Metal HaterZ]] | ||
[[Category:Group Projects]] | [[Category:Group Projects]] | ||
Latest revision as of 05:24, 17 December 2015
Contents
All Files
- All files will be listed here.
- Appropriate way to title files:
- FileName_YYYYMMDD_HMH
Gene Database
Initial Flow Chart
- Initial flow chart for experimental design - File:Experimental Design Flow Chart 20151115 HMH.pptx
Journal Club Presentation Power Points
- Microarray Paper Presentation - File:SoMicroarrayPaperPresentation 20151117 HMH.pptx
- Genome Paper Presentation - File:GenomePPT 20151123 HMH.pdf
Data Processing Notes from Dr. Dahlquist
- Page 1 of Notes - Media:DrDDataProcessNotes1 20151119 HMH.JPG
- Page 2 of Notes - Media:DrDDataProcessNotes2 20151119 HMH.JPG
GenMapp Builder
- Note:This is now outdated.
- File:ShewanellaOneidensisGMBuilder 20151201 HMH.zip
Statistical Analysis Excel Sheets
- Prior to Splitting:
- After splitting, use this one:
- Following the splitting, averages taken and ttests done to data sets:
- File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx
- File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
- UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx
- I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. — Kdahlquist (talk) 15:22, 9 December 2015 (PST)
- Ready for GenMAPP
- .txt file for GenMAPP
- Ranked List from MAPPFinder:
Sanity Check Table
MAPPFinder Documents
- gdb file - File:So-Std 20151201special.zip
- File:ColorSetforExpressionData F60C60 20151210 HMH.gex
- GenMAPP with all comparisons - File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex
- Filtered GO terms for increased - File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx
- Filtered GO terms for decreased - File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx
- Screenshots showing significant results - File:CompiledScreenShots 20151212 HMH.docx
- MAPP for Fatty Acid Degradation - File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp
- Screenshot of results -
- Screenshot of results -
- MAPP for Ribosome - File:Ribosomal Soneidensis 20151213 HMH.mapp
- Screenshot of results -
- Screenshot of results -
- MAPP for Compiled Ribosome - File:Compiled Ribosome 20151216 HMH.mapp
- Screenshot of results -
- Screenshot of results -
- MAPP for Compiled Fatty Acid Degradation -File:Compiled Fatty Acid Degradation 20151216 HMH.mapp
- Screenshot of results -
- Screenshot of results -
KEGG Screenshots
- Fatty Acid Degradation
- Ribosome
Tables for Paper
- Table showing variations between Yang et al. paper for 6 chosen genes and our results - File:Gene Comparison 20151216 HMH.xlsx
- Tale showing variations between Yang et al. paper for genes involved in the ribosome pathway and our results - File:Ribosome Pathway Comparison 20151216 HMH.xlsx
