Emmatyrnauer Week 14 - Revision history

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ clarification

2017-12-15T02:03:25Z

‎Visualizing My Gene Regulatory Network with GRNsight: clarification

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ specification

2017-12-05T23:54:52Z

‎Visualizing My Gene Regulatory Network with GRNsight: specification

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ editing excel workbook

2017-12-05T23:54:04Z

‎Visualizing My Gene Regulatory Network with GRNsight: editing excel workbook

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ adding excel workbook used for GRNsight

2017-12-05T05:07:17Z

‎Visualizing My Gene Regulatory Network with GRNsight: adding excel workbook used for GRNsight

Emmatyrnauer: /* Electronic notebook for the continuation of Week 10 Data Analysis */ adding conclusion

2017-12-05T04:58:44Z

‎Electronic notebook for the continuation of Week 10 Data Analysis: adding conclusion

Emmatyrnauer: /* References */ adding references

2017-12-05T04:38:40Z

‎References: adding references

Emmatyrnauer: adding conclusion, acknowledgements, and references

2017-12-05T03:38:55Z

adding conclusion, acknowledgements, and references

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ personalized electronic notebook

2017-12-05T02:32:20Z

‎Visualizing My Gene Regulatory Network with GRNsight: personalized electronic notebook

Emmatyrnauer: /* Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes */ linked to preserved results from yeastract

2017-12-05T02:31:15Z

‎Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: linked to preserved results from yeastract

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ adding powerpoint link

2017-12-05T02:23:17Z

‎Visualizing My Gene Regulatory Network with GRNsight: adding powerpoint link

@@ Line 48: / Line 48: @@
 #* I named the worksheet containing my organized adjacency matrix "network" and Saved.
 #**File: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
-#**File after edits during class (#5 is the final version): [[Media: REGULATIONMATRIXFINAL_ET.zip]]
+#**File after edits during class--trimming of regulatory network, explained on [[Emmatyrnauer Week 15]] (#5 is the final version): [[Media: REGULATIONMATRIXFINAL_ET.zip]]
 # Now I visualized what these gene regulatory networks look like with the GRNsight software.
 #* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.

@@ Line 48: / Line 48: @@
 #* I named the worksheet containing my organized adjacency matrix "network" and Saved.
 #**File: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
-#**File after edits during class: [[Media: REGULATIONMATRIXFINAL_ET.zip]]
+#**File after edits during class (#5 is the final version): [[Media: REGULATIONMATRIXFINAL_ET.zip]]
 # Now I visualized what these gene regulatory networks look like with the GRNsight software.
 #* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.

@@ Line 48: / Line 48: @@
 #* I named the worksheet containing my organized adjacency matrix "network" and Saved.
 #**File: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
 # Now I visualized what these gene regulatory networks look like with the GRNsight software.
 #* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.

@@ Line 47: / Line 47: @@
 #** I then 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.
 #* I named the worksheet containing my organized adjacency matrix "network" and Saved.
 # Now I visualized what these gene regulatory networks look like with the GRNsight software.
 #* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.

@@ Line 52: / Line 52: @@
 ====Conclusion====
-For the assignment this week,
+For the assignment this week, I used the YEASTRACT database to determine the connection between the regulation of different genes from the profile 45 genelist of the wild type microarray data. Yeastract allowed me to identify similarities in the expression pattern (through transcription factors) of the different genes. From profile 45, 23 transcription factors were identified as significant (these transcription factors regulated the most genes in the genelist of profile 45). I then used YEASTRACT to generate a regulation matrix of the 23 transcription factors--i also added GLN3 per the instructions. Finally, I made some adjustments to this regulation matrix (which was downloaded as a CSV file) to allow for it to be readable by GRNsight. I opened it in GRNsight which generated a graph of my network. This network graphically depicted the connections between the different genes.
 ==Acknowledgements==

@@ Line 63: / Line 63: @@
 ==References==
 #LMU BioDB 2017. (2017). Week 10. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
+#YEASTRACT. Retrieved December 4, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
 {{Emmatyrnauer}}

← Older revision		Revision as of 03:38, 5 December 2017
Line 50:		Line 50:
	#* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.		#* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
	#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network. I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results. I pasted it into my PowerPoint presentation from week 10 and uploaded a new version of the powerpoint including this screenshot to wiki: [[Media:Wt_profileimage_presentation_emmat.pptx]]		#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network. I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results. I pasted it into my PowerPoint presentation from week 10 and uploaded a new version of the powerpoint including this screenshot to wiki: [[Media:Wt_profileimage_presentation_emmat.pptx]]
		+
		+	====Conclusion====
		+	For the assignment this week,
		+
		+	==Acknowledgements==
		+	#Dr. Dahlquist for teaching and assisting me with the data analysis
		+	#The data analyst guild for assisting with the data analysis
		+	# I copied and modified the instructions from the [[Week 10]] assignment page.
		+	While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
		+	[[User:Emmatyrnauer\|Emmatyrnauer]] ([[User talk:Emmatyrnauer\|talk]]) 19:38, 4 December 2017 (PST)
		+
		+	==References==
		+	#LMU BioDB 2017. (2017). Week 10. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
		+	#
		+	{{Emmatyrnauer}}

@@ Line 33: / Line 33: @@
 I analyzed the regulatory matrix file I generated above in Microsoft Excel and visualized it using GRNsight.
-# First I needed to properly format the output files from YEASTRACT.  I repeated these steps for each of the three files I generated above.
+# First I needed to properly format the output file from YEASTRACT.
 #*  I opened the file in Excel.  It did 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.  I then went to the "Data" tab and selected "Text to columns".  In the Wizard that appeared, I selected "Delimited" and clicked "Next".  In the next window, I selected "Semicolon", and clicked "Next".  In the next window, I left the data format at "General", and clicked "Finish".  This now looked 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.
 #* I saved this file in Microsoft Excel workbook format (.xlsx).

@@ Line 19: / Line 19: @@
 #**'''23 transcription factors are green/significant'''
 #* '''''I copied the table of results from the web page and pasted it into a new Excel workbook to preserve the results.'''''
-#** '''''I uploaded the Excel file to wiki linked to it here:.'''''
+#** '''''I uploaded the Excel file to wiki linked to it here: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]].'''''
 #** '''''Is your transcription factor on the list?  If so, what is their "% in user set", "% in YEASTRACT", and "p value".''''' (Note: I didn't answer this because I was assigned the wt strain).
 # For the mathematical model and GRNsight, I needed to define a ''gene regulatory network'' of transcription factors that regulatde other transcription factors.  I used YEASTRACT to assist me with creating the network.  I wanted to generate a network with approximately 15-30 transcription factors in it.

@@ Line 49: / Line 49: @@
 # Now I visualized what these gene regulatory networks look like with the GRNsight software.
 #* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
-#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network.  I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results.  I pasted it into my PowerPoint presentation.
+#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network.  I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results.  I pasted it into my PowerPoint presentation from week 10 and uploaded a new version of the powerpoint including this screenshot to wiki: [[Media:Wt_profileimage_presentation_emmat.pptx]]