Lucia I. Ramirez Week 12: Difference between revisions

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#** Repeat these steps to generate a second regulation matrix, this time applying the Regulations Filter "Documented", "'''Only''' DNA binding evidence".
#** Repeat these steps to generate a second regulation matrix, this time applying the Regulations Filter "Documented", "'''Only''' DNA binding evidence".
#** Repeat these steps a third time to generate a third regulation matrix, this time applying the Regulations Filter "Documented", DNA binding '''and''' expression evidence".
#** Repeat these steps a third time to generate a third regulation matrix, this time applying the Regulations Filter "Documented", DNA binding '''and''' expression evidence".
{{Template: Lucia I. Ramirez}}
[[Category: BIOL398-04/S15]]

Revision as of 17:50, 13 April 2015

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

In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time. The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors. We will explore this using the YEASTRACT database.

  1. Open the gene list in Excel for the profile/cluster that you analyzed for the Week 11 Assignment.
    • Copy the list of gene IDs onto your clipboard.
  2. Launch a web browser and go to the YEASTRACT database.
    • On the left panel of the window, click on the link to Rank by TF.
    • Paste your list of genes from your cluster into the box labeled ORFs/Genes.
    • Check the box for Check for all TFs.
    • Accept the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
    • Do not apply a filter for "Filter Documented Regulations by environmental condition".
    • Rank genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
    • Click the Search button.
  3. Answer 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"?
    • List the "significant" transcription factors on your wiki page, along with the corresponding "% in user set", "% in YEASTRACT", and "p value".
      • Are CIN5, GLN3, HMO1, and ZAP1 on the list?
  4. For the mathematical model that we will build in class, 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 and your partner will need to analyze the same gene regulatory network for your modeling project. Compare the lists of "significant" factors that you and your partner generated. How many of the transcription factors appear in both of your lists? You will use these transcription factors and add CIN5, GLN3, HMO1, and ZAP1 if they are not in your list. Use your discretion to add transcription factors until you reach a list of 15-30 factors. 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 CIN5, GLN3, HMO1, and ZAP1) into both the "Transcription factors" field and the "Target ORF/Genes" field.
    • We are going to generate several regulation matrices, with different "Regulations Filter" options.
      • For the first one, accept the defaults: "Documented", "DNA binding plus expression 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.
      • Repeat these steps to generate a second regulation matrix, this time applying the Regulations Filter "Documented", "Only DNA binding evidence".
      • Repeat these steps a third time to generate a third regulation matrix, this time applying the Regulations Filter "Documented", DNA binding and expression evidence".

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Journals/Assignments

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 14

Week 15

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