Difference between revisions of "Aporras1 Week 15"

Latest revision as of 00:16, 16 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, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG

GRNsight Regulation MATLAB Output

1. Used Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx and allowed Dr. Dahlquist to run MATLAB.
   • Once it was completed, saved the output workbook as:Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx
   • Saved the images and uploaded them to the wiki as:Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip
2. Went to the GRNsight home page.
   • Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.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 and the deliverables, in Project Deliverables, asked for two separate files.
   • 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 stem.xlsx
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)
   • Media:AP YEASTRACT Transcription Factors.xlsx
5. GRNmap input workbook (with network adjacency matrix, .xlsx)
   • Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx
6. GRNmap output workbook (.xlsx)
   • Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx
   • Expression vs Time Images generated from MATLAB
     • Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip
7. Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, & Week 14) 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.
   • Summary for Aporras1_Week_8: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
     • Electronic notebook found in "Electronic Notebook" section of Aporras1_Week_8
   • Summary for Aporras1_Week_10: Used the data from Aporras1_Week_8 to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
     • Electronic notebook found in "Electronic Notebook" section of Aporras1_Week_10
   • Summary for Aporras1_Week_14: Made edits to Aporras1_Week_8 and Aporras1_Week_10 according to feedback from Dr. Dahlquist & Dr. Dionisio. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
     • Electronic notebook found in "Electronic Notebook" section of Aporras1_Week_14.

Final Powerpoint Presentation

Media:JASPAR The Friendly Ghost Group Presentation.pdf

Final Paper/Group Report

JASPAR the Friendly Ghost Final Group Report

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, received in class direction and instruction from Dr. Dahlquist.
4. Met up with group members in JASPAR the Friendly Ghost after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Aporras1 (talk) 16:11, 7 December 2017 (PST)

References

1. Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
2. LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
3. 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
4. Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.