Dmadere Week 10

Methods/Results

Created GRNmap Input Workbook

production_rates sheet

• Created "production_rate" column in Excel workbook.
• Used Microsoft Access database to acquire all data used in analysis.
• Used these steps to perform query:
  1. Imported list of genes to a new table in the database. Clicked on the "External Data" tab and selected the Excel icon with the "up" arrow on it.
  2. Clicked the "Browse" button and selected Excel file containing network that was used to upload to GRNsight.
  3. Made sure the button next to "Import the source data into a new table in the current database" and clicked "OK".
  4. In the next window, selected the "network" worksheet, if it hasn't already been automatically selected. Clicked "Next".
  5. In the next window, made sure the "First Row Contains Column Headings" was checked. Clicked "Next".
  6. In the next window, the left-most column was highlighted. Changed the "Field Name" to "id" if it didn't say that already. Clicked "Next".
  7. In the next window, selected the button for "Choose my own primary key." and chose the "id" field from the drop down next to it. Clicked "Next".
  8. In the next field, made sure it said "Import to Table: network". Clicked Finish.
  9. In the next window did not save import steps, clicked "Close".
  10. A table called "network" appeared in the list of tables at the left of the window.
  11. Went to the "Create" tab. Clicked on the icon for "Query Design".
  12. In the window that appeared, clicked on the "network" table and clicked "Add". Clicked on the "production_rates" table and clicked "Add". Clicked "Close".
  13. The two tables appeared in the main part of the window. Told Access which fields in the two tables correspond to each other by clicking on the word "id" in the network table and dragging mouse to the "standard_name" field in the "production_rates" table, and release. Line appeared between those two words.
  14. Right-clicked on the line between those words and selected "Join Properties" from the menu that appeared. Selected Option "2: Include ALL records from 'network' and only those records from 'production_rates' where the joined fields are equal." Clicked "OK".
  15. Clicked on the "id" word in the "network" table and dragged it to the bottom of the screen to the first column next to the word "Field" and released.
  16. Clicked on the "production_rate" field in the "production_rates" table and dragged it to the bottom of the screen to the second column next to the word "Field" and released.
  17. Right-clicked anywhere in the gray area near the two tables. In the menu that appeared, selected "Query Type > Make Table Query...".
  18. In the window that appeared, name your table "production_rates_1" because couldn't have two tables with the same name in the database. Made sure that "Current Database" was selected and clicked "OK".
  19. Went to the "Query Tools: Menus" tab. Clicked on the exclamation point icon. Window appeared that said how many rows pasted into a new table. Clicked "Yes".
  20. New "production_rates_1" table appeared in the list at the left. Double-clicked on that table name to open it.
  21. Copied the data in this table and pasted it back into Excel workbook. Made sure that when pasting used "Paste Special > Paste values" so that the Access formatting didn't get carried along. 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. Selected the workbook want to export the table to, making sure that "Preserve Access formatting" was not checked. Clicked "OK", clicked "Close".
• If there were missing values, substituted the value 0.1980 for the missing production rates.
• Genes were listed in same order in all sheets of 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 contained two columns (from left to right) entitled "id", and "degradation_rate".
  • The id was an identifier that will be used to identify a particular gene.
  • The "degradation_rate" column contained the absolute value of the degradation rate for the corresponding gene as described above, rounded to four decimal places.
    • To obtain these values, used the same file, Microsoft Access database that was used to obtain the production rates in the first worksheet. Again, copied and pasted the values one-by-one or followed the instructions to execute a query, substituting the appropriate "degradation_rates" table in the query. Noted that you didn't need to re-import your "network" table, just needed to create and execute the query.
• Genes listed in the same order in all the sheets in the Excel workbook.
• Substitute the value 0.0990 for the missing degradation rates.

Data & Files

DM_dCHIN5 GRNmap Input