Difference between revisions of "Aporras1 Week 14"
From LMU BioDB 2017
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#* Went back to the YEASTRACT database and followed the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''. | #* Went back to the YEASTRACT database and followed the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''. | ||
| − | #* | + | #* Copied and pasted the list of transcription factors I identified above into both the "Transcription factors" field and the "Target ORF/Genes" field. |
| − | #* | + | #* Used the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence" |
| − | #** | + | #** Clicked the "Generate" button. |
| − | #** In the results window that | + | #** In the results window that appeared, clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop. |
| + | #*** Uploaded file to wiki as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]] | ||
===Deliverables=== | ===Deliverables=== | ||
Revision as of 23:51, 30 November 2017
User page: Antonio Porras
Team page: JASPAR The Friendly Ghost
Assignment page: Week 14
Contents
Electronic Lab Notebook
Edits to Week 8 & 10
Made edits in the Week 8 and Week 10 electronic notebooks and journal entries in accordance to the feedback given from Dr. Dahlquist and Dr. Dionisio.
- Edits to: Week 8
- Provided exact formulas used in excel.
- Made sure tense was consistent throughout the electronic notebook.
- Corrected powerpoint provided by supplying correct values.
- Extended concluding paragraph.
- Acknowledged source of data and specified acknowledgements.
- Edits to: Week 10
- Included specific filenames.
- Reported definitions for 6 GO terms.
- Interpreted GO terms in terms of cold shock.
- Updated references to include GO term definitions.
- Updated acknowledgements to specify instructions were copied and modified from Week 10 assignment page.
- Included the excel file used for the stem.
- Included the .txt file that was used for the stem.
- Added summary paragraph to the end of the journal entry.
Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes
- Opened the gene list in Excel for profile 22 from my stem analysis.
- Gene list Excel file for profile 22 dZAP1: Media:AP dZAP1 profile22 genelist.xlsx
- Copied the list of gene IDs onto my clipboard.
- Launched a web browser and went to the YEASTRACT database.
- On the left panel of the window, clicked on the link to Rank by TF.
- Pasted the list of genes from profile 22 into the box labeled ORFs/Genes.
- Checked the box for Check for all TFs.
- Accepted the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
- Did not apply a filter for "Filter Documented Regulations by environmental condition".
- Ranked genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
- Clicked the Search button.
- Questions:
- How many transcription factors are green or "significant"?
- 49 transcription factors are green or significant.
- 13 transcription factors are yellow or borderline significant.
- 125 transcription factors are pink or insignificant.
- Copied the table of results from the web page and pasted it into a new Excel workbook.
- Uploaded the Excel file and saved it as "AP YEASTRACT Transcription Factors"
- Is dZAP1 transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
- dZAP1p is on the list.
- 43.03% in user set
- 7.02% in YEASTRACT
- p-value: 2E-15
- dZAP1p is on the list.
- Chose the listed transcription factors from the 49 "significant" TFs and selected 20 with the highest value of "% in user set" because they target a high percentage of the genes within my dataset. Also included two transcription factors, GLN3 & HAP4 as directed by the Week 10 instructions. List of "significant" transcription factors used to run the model:
- GLN3
- HAP4
- Ace2p
- Sfp1p
- Bas1p
- Msn2p
- Yap1p
- Ash1p
- Gcn4p
- Msn4p
- Abf1p
- Cst6p
- Sok2p
- Rpn4p
- Hsf1p
- Zap1p
- Cin5p
- Aft1p
- Spt23p
- Pdr1p
- Met4p
- Arr1p
- Went back to the YEASTRACT database and followed the link to Generate Regulation Matrix.
- Copied and pasted the list of transcription factors I identified above into both the "Transcription factors" field and the "Target ORF/Genes" field.
- Used the "Regulations Filter" options of "Documented", "Only DNA binding evidence"
- Clicked the "Generate" button.
- In the results window that appeared, clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop.
- Uploaded file to wiki as: Media:AP Regulation Matrix profile22 dZAP1.xlsx
- How many transcription factors are green or "significant"?
Deliverables
Acknowledgements
- Recieved help from both Dondi and Dr. Dahlquist from feedback given and instructions given in class.
- Copied and modified the instructions from Week 10.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Aporras1 (talk) 16:53, 28 November 2017 (PST)
References
- LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
- LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
- LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
