Week 9 Individual Journal - Revision history

Jnimmers: Formatting

2019-10-29T23:39:23Z

Formatting

Jnimmers: Formatting fix

2019-10-29T23:38:38Z

Formatting fix

Jnimmers: Formatting for question #3

2019-10-29T23:33:36Z

Formatting for question #3

Jnimmers: Add matrix excel sheet

2019-10-29T23:25:57Z

Add matrix excel sheet

Jnimmers: Update filles with mastersheet

2019-10-29T23:23:33Z

Update filles with mastersheet

Jnimmers: Added figure powerpoint

2019-10-29T23:20:29Z

Added figure powerpoint

Jnimmers: Edit instructions, answer questions

2019-10-29T22:54:42Z

Edit instructions, answer questions

Jnimmers: invoke template

2019-10-29T22:17:37Z

invoke template

Jnimmers: Add week 9 pt.2

2019-10-29T22:15:34Z

Add week 9 pt.2

Jnimmers: Add week 9 pt.2 Instructions

2019-10-29T22:06:44Z

Add week 9 pt.2 Instructions

@@ Line 76: / Line 76: @@
 #** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
-==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes (Tuesday, October 29)====
+=== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes (Tuesday, October 29)===
 In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time.  The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors.  We will explore this using the YEASTRACT database.

@@ Line 67: / Line 67: @@
-##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
+#* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
-##** Each member of the group will be reporting on his or her own cluster in your research presentation.  You should take care to choose terms that are the most significant, but that are also not too redundant.  For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
+#** Each member of the group will be reporting on his or her own cluster in your research presentation.  You should take care to choose terms that are the most significant, but that are also not too redundant.  For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
-##*** Note whether the same GO terms are showing up in multiple clusters.
+#*** Note whether the same GO terms are showing up in multiple clusters.
-##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].  In your research presentation, you will discuss the biological interpretation of these GO terms.  In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?  Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?'''''
+#'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].  In your research presentation, you will discuss the biological interpretation of these GO terms.  In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?  Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?'''''
-##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
+#* To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
-##** Copy and paste the GO ID (e.g. GO:0044848) into the search field on the left of the page.
+#** Copy and paste the GO ID (e.g. GO:0044848) into the search field on the left of the page.
-##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
+#** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
-##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
+#** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
 ==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes (Tuesday, October 29)====

@@ Line 91: / Line 91: @@
 #* Click the ''Search'' button.
 # Answer the following questions:
-#* In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant".  '''''How many transcription factors are green or "significant"?''''' : 3, 6,174.
+#* In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant".  '''''How many transcription factors are green or "significant"?''''' :
 #* '''''Copy the table of results from the web page and paste it into a new Excel workbook to preserve the results.'''''
 #** '''''Upload the Excel file to the wiki and link to it in your electronic lab notebook.'''''
-#** '''''Are CIN5:17.95%, 0.96%, 0,999, GLN3 36.75%, 1.78%, 0.215224764, and/or HAP4 23.08%, 2.47%, 0.008910675 on the list?  If so, what is their "% in user set", "% in YEASTRACT", and "p value".'''''
+#** '''''Are CIN5, GLN3, and/or HAP4 on the list?  If so, what is their "% in user set", "% in YEASTRACT", and "p value".'''''
 # 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 YEASTRACT to assist us with creating the network.  We want to generate a network with approximately 15-20 transcription factors in it.
 #* You need to select from this list of "significant" transcription factors, which ones you will use to run the model.  You will use these transcription factors and add GLN3, HAP4, and CIN5 if they are not in your list.  Explain in your electronic notebook how you decided on which transcription factors to include.  Record the list and your justification in your electronic lab notebook.  Each group member will select a different network (they can have some overlapping transcription factors, but some should also be different).

@@ Line 134: / Line 134: @@
 *[[Media: BIOL367_F19_Jnimmers_p-value_slide.pptx | Powerpoint of all Relavant Figures (P-Value Table and GRNsight)]]
 *[[Media: BIOL367_F19_microarray-data_dGLN3_JNM_1021.xlsx | Mastersheet of All dGLN3 Data & Genelist Yeast Extraction Data]]
 ==Conclusion==

@@ Line 132: / Line 132: @@
 *[[Media: DGLN3_GOlist_JNM.zip ‎ | dGLN3_GOlist Files from STEM]]
 *[[Media: DGLN3_profile9_GOlist_JNM.xlsx| Excel sheet of Profile 9]]
-*[[Media: BIOL367_F19_Jnimmers_p-value_slide.pptx | Powerpoint of all relavant figures (P-Value Table and GRNsight)]]
+*[[Media: BIOL367_F19_Jnimmers_p-value_slide.pptx | Powerpoint of all Relavant Figures (P-Value Table and GRNsight)]]
 ==Conclusion==

← Older revision		Revision as of 22:17, 29 October 2019
Line 136:		Line 136:
	==Acknowledgements==		==Acknowledgements==
	==References==		==References==
		+
		+	{{jnimmers}}

← Older revision		Revision as of 22:15, 29 October 2019
Line 102:		Line 102:
	#** Click the "Generate" button.		#** Click the "Generate" button.
	#** In the results window that appears, click on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appears and save it to your Desktop. Rename this file with a meaningful name so that you can distinguish it from the other files you will generate.		#** In the results window that appears, click on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appears and save it to your Desktop. Rename this file with a meaningful name so that you can distinguish it from the other files you will generate.
		+
		+	==== Visualizing Your Gene Regulatory Networks with GRNsight ====
		+
		+	We will analyze the regulatory matrix files you generated above in Microsoft Excel and visualize them using GRNsight to determine which one will be appropriate to pursue further in the modeling.
		+	# First we need to properly format the output files from YEASTRACT.
		+	#* Open the file in Excel. It will not open properly in Excel because a semicolon was used as the column delimiter instead of a comma. To fix this, Select the entire Column A. Then go to the "Data" tab and select "Text to columns". In the Wizard that appears, select "Delimited" and click "Next". In the next window, select "Semicolon", and click "Next". In the next window, leave the data format at "General", and click "Finish". This should now look like a table with the names of the transcription factors across the top and down the first column and all of the zeros and ones distributed throughout the rows and columns. This is called an "adjacency matrix." If there is a "1" in the cell, that means there is a connection between the trancription factor in that row with that column.
		+	#* Save this file in Microsoft Excel workbook format (.xlsx).
		+	<!--#* Check to see that all of the transcription factors in the matrix are connected to at least one of the other transcription factors by making sure that there is at least one "1" in a row or column for that transcription factor. If a factor is not connected to any other factor, delete its row and column from the matrix. Make sure that you still have somewhere between 15 and 30 transcription factors in your network after this pruning.
		+	#** Only delete the transcription factor if there are all zeros in its column '''AND''' all zeros in its row. You may find visualizing the matrix in GRNsight (below) can help you find these easily.-->
		+	#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), we need to transpose the matrix. Insert a new worksheet into your Excel file and name it "network". Go back to the previous sheet and select the entire matrix and copy it. Go to you new worksheet and click on the A1 cell in the upper left. Select "Paste special" from the "Home" tab. In the window that appears, check the box for "Transpose". This will paste your data with the columns transposed to rows and vice versa. This is necessary because we want the transcription factors that are the "regulatORS" across the top and the "regulatEES" along the side.
		+	#* The labels for the genes in the columns and rows need to match. Thus, delete the "p" from each of the gene names in the columns. Adjust the case of the labels to make them all upper case.
		+	#* In cell A1, copy and paste the text "rows genes affected/cols genes controlling".
		+	#* Finally, for ease of working with the adjacency matrix in Excel, we want to alphabatize the gene labels both across the top and side.
		+	#** Select the area of the entire adjacency matrix.
		+	#** Click the Data tab and click the custom sort button.
		+	#** Sort Column A alphabetically, being sure to exclude the header row.
		+	#** Now sort row 1 from left to right, excluding cell A1. In the Custom Sort window, click on the options button and select sort left to right, excluding column 1.
		+	#* Name the worksheet containing your organized adjacency matrix "network" and Save.
		+	# Now we will visualize what these gene regulatory networks look like with the GRNsight software.
		+	#* Go to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
		+	#* Select the menu item File > Open and select the regulation matrix .xlsx file that has the "network" worksheet in it that you formatted above. If the file has been formatted properly, GRNsight should automatically create a graph of your network. You can click the "Grid Layout" button to arrange the nodes in a grid, or you can click and drag the nodes (genes) around until you get a layout that you like and take a screenshot of the results. Paste it into your PowerPoint presentation.
		+	#** If you have nodes (genes) floating around in the display that are not connected to any other nodes, we need to delete them from the network for the modeling to work properly. Go back to the Excel workbook and network sheet and delete both the row and column with the floating gene's name. Then re-upload the edited file to GRNsight to visualize it. Use this final version in your PowerPoint and subsequent modeling.
		+