Ymesfin Week 10

Purpose

The purpose of this assignment was to create a detailed electronic lab notebook to statistically analyze a DNA microarray dataset, demonstrate our understanding of p-value cut-offs, and display the relationships between the network of transcription factors in Saccharomyces cerevisiae. This week students will create a GRNmap input to further understand the relationship between the genes in Saccharomyces cerevisiae and to familiarize themselves with creating queries and modeling.

Methods

Creating the GRNmap Input Workbook

1. Opened new excel worksheet

production_rates sheet

1. Named first sheet "production_rates" and labeled the first and second columns 'id' and "production_rate", respectively.
2. Downloaded Production Rates Database.
3. 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.
4. Clicked the "Browse" button and selected Excel file containing network used to upload to GRNsight.
5. Made sure the button next to "Import the source data into a new table in the current database" and clicked "OK".
6. In the next window, selected the "network" worksheet, if it wasn't automatically selected. Clicked "Next".
7. In the next window, made sure the "First Row Contains Column Headings" was checked. Clicked "Next".
8. In the next window, changed the "Field Name" to "id". Clicked "Next".
9. 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".
10. In the next field, made sure it said "Import to Table: network". Clicked Finish.
11. Clicked "Close".
12. Went to the "Create" tab. Clicked on the icon for "Query Design".
13. In the window that appeared, clicked on the "network" table and clicked "Add". Clicked on the "production_rates" table and clicked "Add". Clicked "Close".
14. Clicked on the word "id" in the network table and dragged mouse to the "standard_name" field in the "production_rates" table, and released.
15. Right-clicked on the line between those words and selected "Join Properties" from the menu that appears. Selected Option "2: Include ALL records from 'network' and only those records from 'production_rates' where the joined fields are equal." Clicked "OK".
16. 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.
17. 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.
18. Right-clicked anywhere in the gray area near the two tables. In the menu that appeared, selected "Query Type > Make Table Query...".

1. In the window that appeared, named the table "production_rates_1". Made sure that "Current Database" is selected and Clicked "OK".
2. Went to the "Query Tools: Menus" tab. Clicked on the exclamation point icon. A window appeared that tells how many rows were being pasted into a new table. Clicked "Yes".
3. Your new "production_rates_1" table will appear in the list at the left. Double-click on that table name to open it.
4. Copied the data in this table and pasted it back into Excel workbook.
   • If there were missing values, value 0.1980 was substituted for the missing production rates.

Data/Files

GRNmap Input Sheet