Aporras1 Week 14

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User page: Antonio Porras

Team page: JASPAR The Friendly Ghost

Assignment page: Week 14

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

  1. Opened the gene list in Excel for profile 22 from my stem analysis.
    • 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 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.
  3. Questions:
    • How many transcription factors are green or "significant"?
      • 49 transcription factors are green or significant.
      • 13 transcription factors are yellow or borderline significant.
    • Copied the table of results from the web page and pasted it into a new Excel workbook.
      • Upload the Excel file to OWW or Box and link to it in your 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).
  4. 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.

Acknowledgements

  1. Recieved help from both Dondi and Dr. Dahlquist from feedback given and instructions given in class.
  2. 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

  1. LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
  2. LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
  3. LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
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