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.

degradation_rates sheet

• This sheet contains degradation rates for all genes in the network, which are provided by the user.
• Currently, the Dahlquist Lab is using data based on published mRNA half-life data from Neymotin et al. (2006).
  • We converted the half-life data values to the degradation rates by taking the natural log of the half-life and dividing by 2.
• The sheet should contain two columns (from left to right) entitled "id", and "degradation_rate".
  • The id is an identifier that the user will use to identify a particular gene.
  • The "degradation_rate" column should then contain the absolute value of the degradation rate for the corresponding gene as described above, rounded to four decimal places.
    • To obtain these values, you will use the same file, Microsoft Access database that you used to obtain the production rates in the first worksheet. Again, you can copy and paste the values one-by-one or you can follow the instructions to execute a query, substituting the appropriate "degradation_rates" table in the query. Note that you don't need to re-import your "network" table, you just need to create and execute the query.
• Again note, the genes should be listed in the same order in all the sheets in the Excel workbook.
• If there are missing values, substitute the value 0.0990 for the missing degradation rates.

Expression Data Sheets for Individual Yeast Strains

• Expression data can be provided for either a single strain or multiple strains of yeast (for example, the wild type strain and a transcription factor deletion strain).
  • Each strain will have its own sheet in the workbook.
  • Each sheet should be given a unique name that follows the convention "STRAIN_log2_expression", where the word "STRAIN" is replaced by the strain designation, which will appear in the optimization_diagnostics sheet.
    • Everyone in the class will have at least one expression worksheet called "wt_log2_expression".
    • You should have included the transcription factors GLN3, HAP4, and CIN5 in your network. Thus, we will use the expression data from the dGLN3, dHAP4, dCIN5 deletion strains in our workbooks as well, naming the worksheets "dgln3_log2_expression", "dhap4_log2_expression", and "dcin5_expression".
      • If, for some reason, you don't have all three of those genes in your network, only include expression data for the wild type and the genes out of those three that you have in your network.
• The sheet should have the following columns in this order:
  1. "id": list of all genes. The genes should be listed in the same order in all the sheets in the Excel workbook.
  2. The next series of columns should contain the expression data for each gene at a given timepoint given as log2 ratios (log2 fold changes). The column header should be the time at which the data were collected, without any units. For example, the 15 minute timepoint would have a column header "15" and the 30 minute timepoint would have the column header "30". GRNmap supports replicate data for each of the timepoints. Replicate data for the same timepoint should be in columns immediately next to each other and have the same column headers. For example, three replicates of the 15 minute timepoint would have "15", "15", "15" as the column headers.
  3. If data are provided for multiple strains, each strain should have data for the same timepoints, although the number of replicates can vary.
• Include the data for the 15, 30, and 60 minute timepoints, but not the 90 or 120 minute timepoints.
• The data you will be using is contained in the Expression-and-Degradation-rate-database_2019.accdb file that you used to obtain the production and degradation rates.
• It is tedious to copy and paste all of these data by hand, so we will execute a query in Microsoft Access to do it for you. Follow the steps listed for the "production_rates" sheet for each strains expression data. After you import the data into Excel, you will need to change the column headers to "15", "15", etc., as described above.
• Missing values in the expression data sheets are OK; you don't need to put any values there like you did for the production_rates or degradation_rates sheets.

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.