Difference between revisions of "Aporras1 Week 14"
From LMU BioDB 2017
(→Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: uploaded file) |
(renaming) |
||
| Line 28: | Line 28: | ||
===Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes=== | ===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. | # Opened the gene list in Excel for profile 22 from my stem analysis. | ||
| − | #* Gene list Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]] | + | #* Gene list Excel file for profile 22 dZAP1: [[Media:AP dZAP1 profile22 genelist.xlsx]] |
#* Copied the list of gene IDs onto my clipboard. | #* Copied the list of gene IDs onto my clipboard. | ||
# Launched a web browser and went to the [http://www.yeastract.com/ YEASTRACT database]. | # Launched a web browser and went to the [http://www.yeastract.com/ YEASTRACT database]. | ||
| Line 52: | Line 52: | ||
#*** p-value: 2E-15 | #*** p-value: 2E-15 | ||
#* 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|Week 10]] instructions. List of "significant" transcription factors used to run the model: | #* 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|Week 10]] instructions. List of "significant" transcription factors used to run the model: | ||
| − | #** GLN3 | + | #**GLN3 |
| − | #** HAP4 | + | #**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 ''[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]''. | ||
#* Copy and paste the list of transcription factors you identified (plus the transcription factor deleted in your strain) into both the "Transcription factors" field and the "Target ORF/Genes" field. | #* Copy and paste the list of transcription factors you identified (plus the transcription factor deleted in your strain) into both the "Transcription factors" field and the "Target ORF/Genes" field. | ||
Revision as of 23:30, 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.
- Copy and paste the list of transcription factors you identified (plus the transcription factor deleted in your strain) into both the "Transcription factors" field and the "Target ORF/Genes" field.
- We are going to use the "Regulations Filter" options of "Documented", "Only DNA binding evidence"
- Click the "Generate" button.
- In the results window that appears, click on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appears and save it to your Desktop. Rename this file with a meaningful name so that you can distinguish it from the other files you will generate.
- 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
