Difference between revisions of "Aporras1 Week 15"

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(→‎Electronic Notebook: pdr1)
(→‎Electronic Notebook: spt23)
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# Network was determined to be too big.
 
# Network was determined to be too big.
 
#* Began process of deleting the least significant  
 
#* Began process of deleting the least significant  
−
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]]:
+
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
 
#**GLN3
 
#**GLN3
 
#**HAP4
 
#**HAP4
Line 31: Line 31:
 
#**Met4p
 
#**Met4p
 
#**Arr1p
 
#**Arr1p
 +
 +
===ARR1 deletion===
 
# Moved "network" workbook to a new file found in folder "FOLDER NAME": Network ARR1 deletion.xlsx
 
# Moved "network" workbook to a new file found in folder "FOLDER NAME": Network ARR1 deletion.xlsx
 
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
 
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
Line 39: Line 41:
 
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.  
 
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.  
 
# Network remained too large.
 
# Network remained too large.
 +
 +
===MET4 deletion===
 
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in folder "FOLDER NAME": Network MET4 deletion.xlsx
 
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in folder "FOLDER NAME": Network MET4 deletion.xlsx
 
# Began by deleting MET4 in worksheet "network MET4 deletion"
 
# Began by deleting MET4 in worksheet "network MET4 deletion"
Line 47: Line 51:
 
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.  
 
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.  
 
# Network remained too large.
 
# Network remained too large.
 +
 +
===PDR1 deletion===
 
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network PDR1 deletion.xlsx
 
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network PDR1 deletion.xlsx
 
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
 
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
−
#* Deleted row 13 and column M containing MET4 data.
+
#* Deleted row 15 and column O containing MET4 data.
 
# Moved whole spreadsheet to a new worksheet "network"
 
# Moved whole spreadsheet to a new worksheet "network"
 
# Uploaded the file to the wiki page.
 
# Uploaded the file to the wiki page.
 
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
 
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
 
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.  
 
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.  
 +
# Network remained too large.
 +
 +
===SPT23 deletion==
 +
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network SPT23 deletion.xlsx
 +
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
 +
#* Deleted row 15 and column O containing MET4 data.
 +
# Moved whole spreadsheet to a new worksheet "network"
 +
# Uploaded the file to the wiki page.
 +
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
 +
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
 +
# Network remained too large.
  
 
===Deliverables Checklist===
 
===Deliverables Checklist===

Revision as of 00:03, 6 December 2017

User page: Antonio Porras

Team page: JASPAR The Friendly Ghost

Assignment page: Week 15

Electronic Notebook

  1. Network was determined to be too big.
    • Began process of deleting the least significant
  2. Re-downloaded Media:AP YEASTRACT Transcription Factors.xlsx and found the transcription factors which I used in Aporras1_Week_14 ranked from highest % in user set to lowest:
      • GLN3
      • HAP4
      • Ace2p
      • Sfp1p
      • Bas1p
      • Msn2p
      • Yap1p
      • Ash1p
      • Gcn4p
      • Msn4p
      • Abf1p
      • Cst6p
      • Sok2p
      • Rpn4p
      • Hsf1p
      • Zap1p
      • Cin5p
      • Aft1p
      • Spt23p
      • Pdr1p
      • Met4p
      • Arr1p

ARR1 deletion

  1. Moved "network" workbook to a new file found in folder "FOLDER NAME": Network ARR1 deletion.xlsx
  2. Began by deleting ARR1 in worksheet "Network ARR1 deletion"
    • Deleted row 5 and column E containing ARR1 data.
  3. Moved whole spreadsheet to a new worksheet "network"
  4. Uploaded the file to the wiki page.
  5. Went to the GRNsight home page.
    • Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
  6. Network remained too large.

MET4 deletion

  1. Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in folder "FOLDER NAME": Network MET4 deletion.xlsx
  2. Began by deleting MET4 in worksheet "network MET4 deletion"
    • Deleted row 13 and column M containing MET4 data.
  3. Moved whole spreadsheet to a new worksheet "network"
  4. Uploaded the file to the wiki page.
  5. Went to the GRNsight home page.
    • Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
  6. Network remained too large.

PDR1 deletion

  1. Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network PDR1 deletion.xlsx
  2. Began by deleting PDR1 in worksheet "network PDR1 deletion"
    • Deleted row 15 and column O containing MET4 data.
  3. Moved whole spreadsheet to a new worksheet "network"
  4. Uploaded the file to the wiki page.
  5. Went to the GRNsight home page.
    • Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
  6. Network remained too large.

=SPT23 deletion

  1. Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network SPT23 deletion.xlsx
  2. Began by deleting PDR1 in worksheet "network SPT23 deletion"
    • Deleted row 15 and column O containing MET4 data.
  3. Moved whole spreadsheet to a new worksheet "network"
  4. Uploaded the file to the wiki page.
  5. Went to the GRNsight home page.
    • Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
  6. Network remained too large.

Deliverables Checklist

  1. Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
  2. PowerPoint of screenshots of stem results (.pptx)
  3. Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
  4. YEASTRACT "rank by TF" results (.xlsx)
  5. GRNmap input workbook (with network adjacency matrix, .xlsx)
  6. GRNmap output workbook (.xlsx)
  7. Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, and Weeks 11-15) support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
    • Note: make a summary and provide links to individual pages with electronic notebooks.

Acknowledgements

  1. Worked alongside Quinn Lanners to begin gathering deliverables.
  2. Copied the formatting and text from GRNsight_Gene_Page_Project_Deliverables checklist in my checklist category.

References

  1. LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
  2. LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
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