Jcowan4 Journal Week 10

Purpose

The purpose was to build experience with database queries and making models. This was done to prepare us for our final assignment.

Methods

Creating the GRNmap Input Workbook

Now that you have identified the gene regulatory network that you want to model, the next step is to generate the input Excel workbook that you will run in the GRNmap modeling software.

Click here to download a sample workbook on which to base the one specific to your network and microarray data.

Note that when following the instructions below, you need to follow them precisely, to the letter, or GRNmap will return an error.

production_rates sheet

• This sheet contains initial guesses for the production rate parameters, P, for all genes in the network.
• Assuming that the system is in steady state with the relative expression of all genes equal to 1, (P/2) - lambda = 0, where lambda is the degradation rate, is a reasonable initial guess.
• The sheet should contain two columns (from left to right) entitled, "id", "production_rate".
  • The id is an identifier that the user will use to identify a particular gene. In our case, we are using the "StandardName", for example, GLN3.
  • The "production_rate" column should then contain the initial guesses for the P parameter as described above, rounded to four decimal places.
    • The production rates are provided in a Microsoft Access database, which you can download from here.
    • You will perform a query to get the list of production rates for each gene as a group.
    • To perform the query, you will need to follow these steps.
      1. Import a your list of genes to a new table in the database. Click on the "External Data" tab and select the Excel icon with the "up" arrow on it.
      2. Click the "Browse" button and select your Excel file containing your network that you used to upload to GRNsight.
      3. Make sure the button next to "Import the source data into a new table in the current database" and click "OK".
      4. In the next window, select the "network" worksheet, if it hasn't already been automatically selected for you. Click "Next".
      5. In the next window, make sure the "First Row Contains Column Headings" is checked. Click "Next".
      6. In the next window, the left-most column will be highlighted. Change the "Field Name" to "id" if it doesn't say that already. Click "Next".
      7. In the next window, select the button for "Choose my own primary key." and choose the "id" field from the drop down next to it. Click "Next".
      8. In the next field, make sure it says "Import to Table: network". Click Finish.
      9. In the next window you do not need to save the import steps, so just click "Close".
      10. A table called "network" should appear in the list of tables at the left of the window.
      11. Go to the "Create" tab. Click on the icon for "Query Design".
      12. In the window that appears, click on the "network" table and click "Add". Click on the "production_rates" table and click "Add". Click "Close".
      13. The two tables should appear in the main part of the window. We need to tell Access which fields in the two tables correspond to each other. Click on the word "id" in the network table and drag your mouse to the "standard_name" field in the "production_rates" table, and release. You will see a line appear between those two words.
      14. Right-click on the line between those words and select "Join Properties" from the menu that appears. Select Option "2: Include ALL records from 'network' and only those records from 'production_rates' where the joined fields are equal." Click "OK".
      15. Click on the "id" word in the "network" table and drag it to the bottom of the screen to the first column next to the word "Field" and release.
      16. Click on the "production_rate" field in the "production_rates" table and drag it to the bottom of the screen to the second column next to the word "Field" and release.
      17. Right-click anywhere in the gray area near the two tables. In the menu that appears, select "Query Type > Make Table Query...".
      18. In the window that appears, name your table "production_rates_1" because you can't have two tables with the same name in the database. Make sure that "Current Database" is selected and Click "OK".
      19. Go to the "Query Tools: Menus" tab. Click on the exclamation point icon. A window will appear that tells you how many rows you are pasting into a new table. Click "Yes".
      20. Your new "production_rates_1" table will appear in the list at the left. Double-click on that table name to open it.
      21. You can copy the data in this table and paste it back into your Excel workbook. Make sure that when you paste that you use "Paste Special > Paste values" so that the Access formatting doesn't get carried along. You can also choose to export this table to Excel going to the "External Data" tab and selecting the Excel icon with the arrow pointing to the right. Select the workbook you want to export the table to, making sure that "Preserve Access formatting" is not checked. Click "OK", click "Close".
• If there are missing values, substitute the value 0.1980 for the missing production rates.
• Note that the genes should be listed in the same order in all the sheets in the Excel workbook.

Data and Files

GRN Map

References

• Gene Ontology Resource. (2019). Retrieved October 30, 2019, from http://geneontology.org/.

• Yeastract+. (2019). Retrieved October 30, 2019, from http://www.yeastract.com/formregmatrix.php.

• GRNsight Home. (2019). Retrieved October 30, 2019, from https://dondi.github.io/GRNsight/.

• LMU BioDB 2019. (2019). Week 9. Retrieved October 30, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9.