Difference between revisions of "Ymesfin Week 10"
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==Methods== | ==Methods== | ||
| + | ===Creating the GRNmap Input Workbook=== | ||
| + | ===production_rates sheet=== | ||
| + | #Downloaded [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/Expression-and-Degradation-rate-database_2019.accdb Production Rates Database.] | ||
| + | #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. | ||
| + | #Clicked the "Browse" button and selected Excel file containing network used to upload to GRNsight. | ||
| + | # Made sure the button next to "Import the source data into a new table in the current database" and clicked "OK". | ||
| + | # In the next window, selected the "network" worksheet, if it wasn't automatically selected. Clicked "Next". | ||
| + | # In the next window, made sure the "First Row Contains Column Headings" was checked. Clicked "Next". | ||
| + | # In the next window, changed the "Field Name" to "id". Clicked "Next". | ||
| + | # 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". | ||
| + | # In the next field, made sure it said "Import to Table: network". Clicked Finish. | ||
| + | # Clicked "Close". | ||
| + | # Went to the "Create" tab. Clicked on the icon for "Query Design". | ||
| + | # In the window that appeared, clicked on the "network" table and clicked "Add". Clicked on the "production_rates" table and clicked "Add". Clicked "Close". | ||
| + | # Clicked on the word "id" in the network table and dragged mouse to the "standard_name" field in the "production_rates" table, and released. | ||
| + | # 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". | ||
| + | # 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. | ||
| + | # 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. | ||
| + | # Right-clicked anywhere in the gray area near the two tables. In the menu that appeared, selected "Query Type > Make Table Query...". | ||
| + | |||
| + | # In the window that appeared, named the table "production_rates_1". Made sure that "Current Database" is selected and Clicked "OK". | ||
| + | # 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". | ||
| + | # Your new "production_rates_1" table will appear in the list at the left. Double-click on that table name to open it. | ||
| + | # Copied the data in this table and pasted it back into Excel workbook. | ||
| + | #* If there were missing values, value </code>0.1980</code> was substituted for the missing production rates. | ||
| + | |||
==Data/Files== | ==Data/Files== | ||
[[Media: Ymesfin_dHAP4_profile48_GRNmap_Input.xlsx | GRNmap Input Sheet]] | [[Media: Ymesfin_dHAP4_profile48_GRNmap_Input.xlsx | GRNmap Input Sheet]] | ||
Revision as of 18:50, 1 November 2019
Contents
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
production_rates sheet
- Downloaded Production Rates Database.
- 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.
- Clicked the "Browse" button and selected Excel file containing network used to upload to GRNsight.
- Made sure the button next to "Import the source data into a new table in the current database" and clicked "OK".
- In the next window, selected the "network" worksheet, if it wasn't automatically selected. Clicked "Next".
- In the next window, made sure the "First Row Contains Column Headings" was checked. Clicked "Next".
- In the next window, changed the "Field Name" to "id". Clicked "Next".
- 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".
- In the next field, made sure it said "Import to Table: network". Clicked Finish.
- Clicked "Close".
- Went to the "Create" tab. Clicked on the icon for "Query Design".
- In the window that appeared, clicked on the "network" table and clicked "Add". Clicked on the "production_rates" table and clicked "Add". Clicked "Close".
- Clicked on the word "id" in the network table and dragged mouse to the "standard_name" field in the "production_rates" table, and released.
- 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".
- 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.
- 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.
- Right-clicked anywhere in the gray area near the two tables. In the menu that appeared, selected "Query Type > Make Table Query...".
- In the window that appeared, named the table "production_rates_1". Made sure that "Current Database" is selected and Clicked "OK".
- 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".
- Your new "production_rates_1" table will appear in the list at the left. Double-click on that table name to open it.
- 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.
