Dbashour Week 14 - Revision history

Dbashour at 00:15, 10 December 2017

2017-12-10T00:15:26Z

Dbashour: added template

2017-12-09T23:48:08Z

added template

Dbashour: /* Week 10 Continued */ updated TF list

2017-12-09T23:43:32Z

‎Week 10 Continued: updated TF list

Dbashour: added summary

2017-12-09T23:31:23Z

added summary

Dbashour: /* Electronic Notebook */ removed week 8 and 9 methods corrections and put them in corresponding weeks

2017-12-09T21:54:05Z

‎Electronic Notebook: removed week 8 and 9 methods corrections and put them in corresponding weeks

Show changes

Dbashour: added signature and acknowledgements and references

2017-12-09T21:20:26Z

added signature and acknowledgements and references

Dbashour: /* Deliverables */ updated

2017-12-08T06:41:41Z

‎Deliverables: updated

Dbashour: /* Deliverables */ added stem results powerpoint

2017-12-08T06:40:48Z

‎Deliverables: added stem results powerpoint

Dbashour: /* Visualizing Your Gene Regulatory Networks with GRNsight */ updated

2017-12-08T06:27:47Z

‎Visualizing Your Gene Regulatory Networks with GRNsight: updated

Dbashour: syntax

2017-12-08T06:10:24Z

syntax

@@ Line 13: / Line 13: @@
 * added stem worksheet
 * made name of powerpoint more specific with initials and strain name
 ==Week 10 Continued==

@@ Line 4: / Line 4: @@
 * switched the Bonferroni and B-H p value numbers
 * recorded number of replicates, number of NA replaced, and strain
 ==Week 10 Corrections==
 * put electronic notebook in the past tense.
+* added template
 ==Week 10 Continued==
@@ Line 111: / Line 116: @@
 #LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 #Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

@@ Line 32: / Line 32: @@
 #*** '''''My transcription factor is on the list. It's % in user set is 0.3085%, its % in yeastract is 0.1044%, and its p value is 1E-13.
 # For the mathematical model and GRNsight, 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 15-30 transcription factors in it.
-#* I chose all 30 of the significant transcription factors on my list, adding HAP4 since it was not already on the list. I chose these transcription factors among the rest because they are all significant so this way I can analyze all the significant TFs keeping in mind their % in user set, % in yeastract, and p value. All 30 TFs are listed below.
+#* I chose 15 of the significant transcription factors on my list, adding HAP4 since it was not already on the list and CIN5. I chose these transcription factors among the rest because they are all significant and I kept in mind their % in user set, % in yeastract, and p value. All 15 TFs are listed below.
-#**Sfp1p
+#**ACE2
-#** Msn2p
+#**CIN5
-#**Yhp1p
+#**GLN3
-#**Yox1p
+#**HAP4
-#**Ace2p
+#**MSN2
-#**Gln3p
+#**PDR1
-#**Yap1p
+#**PDR3
-#**Pdr3p
+#**SFP1
-#**Ume6p
+#**SWI5
-#** Pdr1p
+#**UME6
-#** Stb5p
+#**YAP1
-#** Swi5p
+#**YHP1
-#** YLR278C
+#**YLR278C
-#** Mig2p
+#**YOX1
-#** Asg1p
+#**ZAP1
-#** Tup1p
 #* I then went to the link ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]'' on the yeastract database and copied and pasted the list of transcription factors above into both the "Transcription factors" field and the "Target ORF/Genes" field.
 #* We are going to use the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"

@@ Line 108: / Line 108: @@
 [[Media:GRNmap_dGLN3_input.xlsx | GRNmap dGLN3 input]] <br>
 [[Media:GRNmap_dGLN3_output.png | GRNmap dGLN3 output]]
 = Acknowledgements =
 # Recieved help from both [[User:Dondi|Dondi]] and [[User:Kdahlquist|Dr. Dahlquist]] from feedback given and instructions given in class.
 # Copied and modified the instructions from [[Week 8]] and [[Week 10|Week 10]] as well as retrieved deliverable file from [[Week 8]]
-# Texted the data analyst group chat for questions including: [[User:Mbalducc|Mary Balducci]], [[User:dbashour|Dina Bashoura]], and [[User:Emmatyrnauer|Emma Tyrnauer]].
+# Texted the data analyst group chat for questions
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' <br>

← Older revision		Revision as of 21:20, 9 December 2017
Line 272:		Line 272:
	[[Media:GRNmap_dGLN3_input.xlsx \| GRNmap dGLN3 input]] <br>		[[Media:GRNmap_dGLN3_input.xlsx \| GRNmap dGLN3 input]] <br>
	[[Media:GRNmap_dGLN3_output.png \| GRNmap dGLN3 output]]		[[Media:GRNmap_dGLN3_output.png \| GRNmap dGLN3 output]]
		+
		+	= Acknowledgements =
		+	# Recieved help from both [[User:Dondi\|Dondi]] and [[User:Kdahlquist\|Dr. Dahlquist]] from feedback given and instructions given in class.
		+	# Copied and modified the instructions from [[Week 8]] and [[Week 10\|Week 10]] as well as retrieved deliverable file from [[Week 8]]
		+	# Texted the data analyst group chat for questions including: [[User:Mbalducc\|Mary Balducci]], [[User:dbashour\|Dina Bashoura]], and [[User:Emmatyrnauer\|Emma Tyrnauer]].
		+
		+	'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' <br>
		+	[[User:Dbashour\|Dbashour]] ([[User talk:Dbashour\|talk]]) 13:20, 9 December 2017 (PST)
		+	= References =
		+	#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
		+	#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
		+	#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
		+	#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
		+	#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

@@ Line 268: / Line 268: @@
 [[Media:DGLN3_ANOVA_DB.xlsx | DGLN3 ANOVA/Stem]] <br>
 [[Media:DGLN3_ppt_Dina.pptx | DGLN3 ppt Dina]] <br>
 [[Media:Gene_List_GO_List_DB.zip | DGLN3 Gene List and GO list]] <br>
 [[Media:Yeastract_results_TF_DB_Gene_hAPI.xlsx | Yeastract TF List]] <br>
 [[Media:GRNmap_dGLN3_input.xlsx | GRNmap dGLN3 input]] <br>
 [[Media:GRNmap_dGLN3_output.png | GRNmap dGLN3 output]]

@@ Line 236: / Line 236: @@
 ====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.
+I will analyze the regulatory matrix files I 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.  You will repeat these steps for each of the three files you generated above.
+# First I need to properly format the output files from YEASTRACT.  I will repeat these steps for each of the three files I generated above.
-#*  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.
+#*  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, I selected the entire Column A.  Then went to the "Data" tab and selected "Text to columns".  In the Wizard that appears, I selected "Delimited" and clicked "Next".  In the next window, I selected "Semicolon", and clicked "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).
+#* I saved this file in Microsoft Excel workbook format (.xlsx).
 #* I checked 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, it was deleted, making sure that I still had somewhere between 15 and 30 transcription factors in my 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.
+#** I 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.
+#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), I needed to transpose the matrix.  I inserted a new worksheet into my Excel file and named it "network".  I went back to the previous sheet and selected the entire matrix and copied it.  I went to you new worksheet and clicked on the A1 cell in the upper left. I selected "Paste special" from the "Home" tab.  In the window that appears, I checked 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.
+#* The labels for the genes in the columns and rows need to match. Thus, I deleted the "p" from each of the gene names in the columns.  I adjusted 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".
+#* In cell A1, I copied and pasted 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.
+#* Finally, for ease of working with the adjacency matrix in Excel, I wanted to alphabatize the gene labels both across the top and side.
-#** Select the area of the entire adjacency matrix.
+#** I selected the area of the entire adjacency matrix.
-#** Click the Data tab and click the custom sort button.
+#** I clicked the Data tab and clicked the custom sort button.
-#** Sort Column A alphabetically, being sure to exclude the header row.
+#** I sorted 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.
+#** Then I sorted row 1 from left to right, excluding cell A1.  In the Custom Sort window, I clicked on the options button and selected sort left to right, excluding column 1.
-#* Name the worksheet containing your organized adjacency matrix "network" and Save.
+#* I named the worksheet containing my organized adjacency matrix "network" and saved it.
-# Now we will visualize what these gene regulatory networks look like with the GRNsight software.
+# Now I visualized what these gene regulatory networks look like with the GRNsight software.
-#* Go to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
+#* I went 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.  Move 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.
+#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that has the "network" worksheet in it that I formatted above.  If the file has been formatted properly, GRNsight should automatically create a graph of your network.  I moved the nodes (genes) around until I got a layout that I liked and took a screenshot of the results and pasted it into my powerpoint presentation.
 ==== Summary of what you need to turn in for the individual Week 10 assignment ====

@@ Line 160: / Line 160: @@
 ##** I copied and pasted the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
 ##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, I click on the button that says "Link to detailed information about <term>, in this case "biological phase"". Here are the results:
-###**small molecule metabolic process - The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule <br>
+###* small molecule metabolic process - The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule <br>
 ###**http://amigo.geneontology.org/amigo/term/GO:0044281
 ###* organic acid catabolic process - The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage<br>