Mbalducc Week 14

Files

Excel Sheet of Profile #22 TF from YEASTRACT

Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes

1. Opened the gene list in Excel for the one of the significant profiles from my stem analysis. I chose a cluster with a clear cold shock/recovery up/down or down/up pattern.
   • Copied the list of gene IDs onto my clipboard.
2. 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 my list of genes from my cluster 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.
3. Answered the following questions:
   • In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant". How many transcription factors are green or "significant"?
     • 43 are green.
   • Copied the table of results from the web page and pasteed it into a new Excel workbook to preserve the results.
     • Uploaded the Excel file to OWW or Box and linked to it in my electronic lab notebook.
     • Is your transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value". (Note that this doesn't apply to the wt strain).
       • My transcription factor, Cin5 was on the list. Here is the data associated with it:
         • % in user set: 40.68%
         • % in YEASTRACT: 3.30%
         • p-value: 0.001495074628175
   • List of 20 significant transcription factors:
     1. Aft2p
     2. Mga2p
     3. Gis1p
     4. Hot1p
     5. Sut1p
     6. Zap1p
     7. Mig1p
     8. Hap2p
     9. Sut2p
     10. Bas1p
     11. Pho2p
     12. Opi1p
     13. Ert1p
     14. Oaf1p
     15. Sfp1p
     16. Mig3p
     17. Rlm1p
     18. Sum1p
     19. Ace2p
     20. Pho4p
   • Went back to the YEASTRACT database and followed the link to Generate Regulation Matrix.
   • Copied and pasted the list of transcription factors I identified (plus the transcription factor deleted in my strain: Cin5p) into both the "Transcription factors" field and the "Target ORF/Genes" field.
   • I used the "Regulations Filter" options of "Documented", "Only DNA binding evidence"
     • Clicked the "Generate" button.
     • In the results window that appeared, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop. I renamed this file with a meaningful name so that I could distinguish it from the other files I will generate.

Acknowledgements

I worked with the rest of the Data Analyst guild: Antonio Porras, Dina Bashoura, and Emma Tyrnauer on this assignment. We spoke in class and created a group chat so we could ask each other questions and help each other as we worked on the project. I also used the instructions from the Week 10 assignment. I edited the instructions slightly so they would be specific to the profile I chose and the procedure I followed.

References

LMU BioDB 2017. (2017). Week 10 Retrieve November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10