Ntesfaio Week 10

Purpose

The purpose of this week's assignment was to create a GRNmap with different sheets that go over the gene that was isolated from STEM profile. We also used GRNsight to visualize the results.

Methods

production_rates sheet

• This sheet contained 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 contained two columns (from left to right) entitled, "id", "production_rate".

• The id was an identifier that the user used to identify a particular gene. In our case, we used the "StandardName", for example, GLN3.

• The "production_rate" column contained the initial guesses for the P parameter as described above, rounded to four decimal places.

• The production rates were provided in a Microsoft Access database

• I performed a query to get the list of production rates for each gene as a group.

• I Imported a list of genes to a new table in the database. I clicked on the "External Data" tab and selected the Excel icon with the "up" arrow on it.

• I clicked the "Browse" button and selected the Excel file containing the network that was used to upload to GRNsight.

• The button next to "Import the source data into a new table in the current database" was selected and I clicked "OK".

• In the next window, I selected the "network" worksheet, if it wasn't already automatically selected. I Clicked "Next".

• In the next window, I made sure the "First Row Contains Column Headings" was checked and I clicked "Next".

• In the next window, the left-most column was highlighted. I changed the "Field Name" to "id". I clicked "Next".

• In the next window, I selected the button for "Choose my own primary key." and chose the "id" field from the drop down next to it. I clicked "Next".

• In the next field, I made sure it said "Import to Table: network". I clicked Finish.

• In the next window I clicked "Close".

• A table called "network" appeared in the list of tables at the left of the window.

• I went to the "Create" tab. I clicked on the icon for "Query Design".

• In the window that appeared, I clicked on the "network" table and clicked "Add". I Clicked on the "production_rates" table and clicked "Add". Lastly I clicked "Close".

• The two tables should appear in the main part of the window. I clicked on the word "id" in the network table and dragged my mouse to the "standard_name" field in the "production_rates" table, and released.

• I Right-clicked on the line between those words and selected "Join Properties" from the menu that appeared.

Selecting Option "2: Include ALL records from 'network' and only those records from 'production_rates' where the joined fields are equal." Click "OK".

• I 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.

• I 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.

• I Right-clicked anywhere in the gray area near the two tables. In the menu that appeared, I selected "Query Type > Make Table Query...".

• In the window that appeared, I named the table "production_rates_1", made sure"Current Database" was selected and Clicked "OK".

• I went to the "Query Tools: Menus" tab. I Clicked on the exclamation point icon. A window appeared that said there are many rows being pasted into a new table. I Clicked "Yes".

The new "production_rates_1" table appeared in the list at the left. I Double-clicked on that table name to open it.

I copied the data in this table and pasted it back into the Excel workbook. I made sure that when I pasted that I used "Paste Special > Paste values" so that the Access formatting doesn't get carried along. I selected the workbook to export the table to, making sure that "Preserve Access formatting" was not checked. I Clicked "OK", clicked "Close".

If there were 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 contained degradation rates for all genes in the network, which are provided by the user.

• The sheet contained two columns (from left to right) entitled "id", and "degradation_rate".

• The id was an identifier that the user used 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, Microsoft Access database that was used to obtain the production rates in the first worksheet. Again, I copy and pasted the values one-by-one

• 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.

Acknowledgments

My homework partners this week are Aby User:Ymesfin and David User:Dramir36. We worked together on running the different databases such as GRNmap and YEASTRACT.

Data and Files

Excel workbook for Week 10

Zipped file of outputs

Bio DB Home page

Template:Ntesfaio

Week 1

User:Ntesfaio

Class Journal Week 1

Week 2

Ntesfaio Week 2

Class Journal Week 2

Week 3

RAD53 / YPL153C Week 3

Class Journal Week 3

Week 4

Ntesfaio Week 4

Class Journal Week 4

Week 5

DrugCentral Week 5

Class Journal Week 5

Week 6

Ntesfaio Week 6

Class Journal Week 6

Week 7

Ntesfaio Week 7

Class Journal Week 7

Week 8

Ntesfaio Week 8

Class Journal Week 8

Week 9

Ntesfaio Week 9

Class Journal Week 9

Week 10

Ntesfaio Week 10

Week 11

Ntesfaio Week 11

Sulfiknights

Week 12/13

Ntesfaio Week 12/13

Sulfiknights

Sulfiknights Deliverables

Ntesfaio Week 15

Ntesfaio Final Individual Reflection