Difference between revisions of "Aporras1 Week 15"

Revision as of 00:00, 8 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 Media:Trimming Network transcription factor deletions dZAP1.zip: 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 Media:Trimming Network transcription factor deletions dZAP1.zip: 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 Media:Trimming Network transcription factor deletions dZAP1.zip: Network PDR1 deletion.xlsx
2. Began by deleting PDR1 in worksheet "network PDR1 deletion"
   • Deleted row 15 and column O containing PDR1 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 & BAS1 deletion

1. Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder Media:Trimming Network transcription factor deletions dZAP1.zip: Network SPT23 deletion.xlsx
2. Began by deleting PDR1 in worksheet "network SPT23 deletion"
   • Deleted row 19 and column S containing SPT23 data.
   • BAS1 transcription factor became disconnected.
   • Deleted row 6 and column F containing BAS1 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.

Network Files After Trimming

Media:Trimming Network transcription factor deletions dZAP1.zip

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by Dr. Dahlquist.

Antonio, I finished paring down the network. Here is the final file (renamed): 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx. — Kdahlquist (talk) 15:55, 6 December 2017 (PST)

GRNsight Visualization

1. Downloaded Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx provided by Dr. Dahlquist.
2. Went to the GRNsight home page.
   • Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved the screenshot as GRNsight Visualization of dZAP1. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved the screenshot as Media:GRNsight Visualization of dZAP1.PNG

Edits to Organization of Files

1. In Week 10 the powerpoint STEM screenshots, GOlists, and genelists were all zipped in Media:AP dZAP1 STEM Profiles and Powerpoint.zip.
   • Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: Media:AP dZAP1 STEM Screenshots & p-values.zip.
   • Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: Media:AP dZAP1 GOlist and genelist for profiles.zip

Deliverables Checklist

1. Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
   • Media:AP dZAP1.zip
2. PowerPoint of screenshots of stem results (.pptx)
   • Media:AP dZAP1 STEM Screenshots & p-values.zip
3. Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
   • Media:AP dZAP1 GOlist and genelist for profiles.zip
4. YEASTRACT "rank by TF" results (.xlsx)
5. GRNmap input workbook (with network adjacency matrix, .xlsx)
   • Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.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.
3. Received file used for GRNsight visualization from Dr. Dahlquist.

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