Heavy Metal HaterZ Files

All Files

• All files will be listed here.
• Appropriate way to title files:
  • FileName_YYYYMMDD_HMH

Gene Database

• File:So-Std HMH 20151214.zip

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• Note:This is now outdated.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:
  1. File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx
  2. File:UpdatedCompiledRawData 20151206 HMH.xlsx
• After splitting, use this one:
  1. UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx
• Following the splitting, averages taken and ttests done to data sets:
  1. File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx
  2. 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
  • File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx
• .txt file for GenMAPP
  • File:CompiledRawData ForGenMAPP 20151208 HMH.txt
• Ranked List from MAPPFinder:

Sanity Check Table

• File:Sanity Check Chart 20151212 HMH.xlsx

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
  • 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
• MAPP for Fatty Acid Degradation - File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp
  • Screenshot of results -
• MAPP for Ribosome - File:Ribosomal Soneidensis 20151213 HMH.mapp
  • Screenshot of results -
• MAPP for Compiled Ribosome - File:Compiled Ribosome 20151216 HMH.mapp
  • Screenshot of results -
• MAPP for Compiled Fatty Acid Degradation -File:Compiled Fatty Acid Degradation 20151216 HMH.mapp
  • 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