Week 10 - Revision history

Kdahlquist: /* Clustering and GO Term Enrichment with stem */ add comment about GO term enrichment

2024-04-04T21:55:26Z

‎Clustering and GO Term Enrichment with stem: add comment about GO term enrichment

2024-03-31T00:29:41Z

‎Reflect: changed from week 6 to week 10

2024-03-26T01:55:07Z

‎Creating the GRNmap Input Workbook: add date

2024-03-26T01:54:40Z

add info on interim deadline

2024-03-26T01:54:02Z

‎Creating the GRNmap Input Workbook: add interim deadline

2024-03-26T01:52:34Z

‎Creating and Visualizing Your Gene Regulatory Network with GRNsight: add date

2024-03-26T01:52:02Z

‎Data and Files: add quality check

2024-03-26T01:44:37Z

‎Creating and Visualizing Your Gene Regulatory Network with GRNsight: add bold/italics

2024-03-26T01:44:16Z

‎Data and Files: added more files

2024-03-26T01:42:35Z

‎Creating the GRNmap Input Workbook: quality control instructions

@@ Line 70: / Line 70: @@
 ==== Clustering and GO Term Enrichment with stem ====
+<!-- NOTE THAT STEM DOES NOT SHOW GO TERM NAMES IN THE RESULTS, NEED TO DO ENRICHMENT ELSWHERE!-->
 # '''Prepare your microarray data file for loading into STEM.'''
 #* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".

@@ Line 225: / Line 225: @@
 === Reflect ===
-Answer the following questions on the Class Journal Week 6 page after you have completed the individual assignment.
+Answer the following questions on the Class Journal Week 10 page after you have completed the individual assignment.
 # What aspect of this assignment came most easily to you?

@@ Line 166: / Line 166: @@
 #* Export the network image by going to the Export menu and selecting "Export Image > To PNG".  '''''Upload the file to the wiki and display it on your individual journal page.'''''
-==== Creating the GRNmap Input Workbook ====
+==== Creating the GRNmap Input Workbook (Tuesday, March 26)====
 We will also use GRNsight to automatically generate the input workbook for the GRNmap modeling software.  '''Note that this feature is still under development, and we will be performing quality control on the exported workbook.'''

@@ Line 3: / Line 3: @@
 '''''There is an interim deadline of 12:01am on Tuesday, March 26 to complete the [[Week_10#Clustering_and_GO_Term_Enrichment_with_stem | stem analysis]] and upload your files.'''''
-'''''Work to be completed by an interim deadline of 12:01am on Tuesday, April 2 will be announced in class next week.'''''
+'''''There is an interim deadline of 12:01am on Tuesday, April 2 to complete up to creating your GRNmap input workbook.'''''
 == Objectives ==

@@ Line 194: / Line 194: @@
 #** Copy the entire content of the "network" sheet into the "network_weights" sheet.
 # '''''Save and upload your Excel Workbook to the wiki and link to it on your individual journal page.'''''  Dr. Dahlquist will run your input workbook in the GRNmap modeling software over the break.
 ==== Data and Files ====

@@ Line 149: / Line 149: @@
 #** '''''Are CIN5 or GLN3 on the list?  If so, what is their "% in user set", "% in YEASTRACT", and "p value"?'''''
-==== Creating and Visualizing Your Gene Regulatory Network with GRNsight ====
+==== Creating and Visualizing Your Gene Regulatory Network with GRNsight (Tuesday, March 26)====
 For the mathematical model that we will build, we need to define a ''gene regulatory network'' of transcription factors that regulate other transcription factors.  We can use GRNsight to assist us with creating the network.  We want to generate a network with approximately 15-20 connected transcription factors in it.

@@ Line 206: / Line 206: @@
 * The zipped together genelist and GOlist files for each of your significant profiles.
 * The .png file showing your gene regulatory network.
-* Your exported Excel workbook from GRNsight beta.
+* Your exported and quality-checked Excel workbook from GRNsight beta.
 ==== Conclusion (Summary Paragraph) ====

@@ Line 164: / Line 164: @@
 #* '''''Record in your electronic lab notebook the number of genes and edges in your network (found at the upper right of the menu bar).'''''
 # Under the "Layout" section, click on the "Grid Layout" button.
-#* Export the network image by going to the Export menu and selecting "Export Image > To PNG".  Upload the file to the wiki and display it on your individual journal page.
+#* Export the network image by going to the Export menu and selecting "Export Image > To PNG".  '''''Upload the file to the wiki and display it on your individual journal page.'''''
 ==== Creating the GRNmap Input Workbook ====

@@ Line 199: / Line 199: @@
 Your data and files section should include:
 * Your Excel workbook with all of your calculations.
 ** Note that you will be working with this workbook for the next week or two, adding computations to it.  Save the <u>new versions</u> to the wiki with the '''same filename'''.  The wiki will store each version of the file so you can always go back to a previous version, if need be.
 * Your PowerPoint slide with a summary table of p values, <u>updated with the screenshots from the stem software</u>.
@@ Line 204: / Line 205: @@
 * The input .txt file that you used to run stem.
 * The zipped together genelist and GOlist files for each of your significant profiles.
 ==== Conclusion (Summary Paragraph) ====

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 ==== Creating the GRNmap Input Workbook ====
-We will also use GRNsight to automatically generate the input workbook for the GRNmap modeling software.
+We will also use GRNsight to automatically generate the input workbook for the GRNmap modeling software.  '''Note that this feature is still under development, and we will be performing quality control on the exported workbook.'''
 # With your final network still open in GRNsight, select from the Export menu "Export Data > To Excel".  In the window that appears, select the following:
 #* Under "Select the Expression Data Source:", choose "Dahlquist_2018"
 #* Under "Select Workbook Sheets to Export:", select the following:
-#** "network"
+#** Network sheets
-#** "network_weights"
+#*** "network"
-#** "degradation_rates"
+#** Expression sheets
-#** "optimization_parameters"
+#*** dcin5_log2_expression
-#** "production_rates"
+#*** dgln3_log2_expression
-#** "threshold_b"
+#*** wt_log2_expression
 #* Click the "Export Workbook" button.
 # Open your workbook in Excel to perform quality control.  Check that it has the following sheets with the following content:
 ==== Data and Files ====