Mbalducc Week 14

Files

Excel Sheet of Profile #38 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"?
     • 0 p-values were colored green, 1 was colored yellow.
   • Copied the table of results from the web page and pasteed it into a new Excel workbook to preserve the results.

1. • • 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).
2. For the mathematical model and GRNsight, we need to define a gene regulatory network of transcription factors that regulate other transcription factors. We can use YEASTRACT to assist us with creating the network. We want to generate a network with approximately 15-30 transcription factors in it.
   • You need to select from this list of "significant" transcription factors, which ones you will use to run the model. You will use these transcription factors and add GLN3 and HAP4 if they are not in your list. Explain in your electronic notebook how you decided on which transcription factors to include. Record the list and your justification in your electronic lab notebook.
   • Go back to the YEASTRACT database and follow 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.

References

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