Aporras1 Week 14 - Revision history

Aporras1: /* Summary Paragraph */ summary paragraph

2017-12-04T01:47:13Z

‎Summary Paragraph: summary paragraph

Aporras1: changed headers

2017-12-04T01:33:50Z

changed headers

Aporras1: /* Summary Paragraph */ changed header style

2017-12-04T01:32:59Z

‎Summary Paragraph: changed header style

Aporras1: summary paragraph header

2017-12-04T01:32:32Z

summary paragraph header

Aporras1: /* Visualizing Your Gene Regulatory Networks with GRNsight */ past tense

2017-12-04T01:29:30Z

‎Visualizing Your Gene Regulatory Networks with GRNsight: past tense

Aporras1: /* Acknowledgements */ acknowledging other data analysts

2017-12-04T00:24:55Z

‎Acknowledgements: acknowledging other data analysts

Aporras1: /* References */ alphabetical order

2017-12-04T00:21:35Z

‎References: alphabetical order

Aporras1: /* References */ yeastract and grnsight

2017-12-04T00:20:51Z

‎References: yeastract and grnsight

Aporras1: /* Deliverables */ screenshot and network file

2017-12-04T00:15:56Z

‎Deliverables: screenshot and network file

Aporras1: /* Visualizing Your Gene Regulatory Networks with GRNsight */ up until network

2017-12-04T00:02:46Z

‎Visualizing Your Gene Regulatory Networks with GRNsight: up until network

← Older revision		Revision as of 01:47, 4 December 2017
Line 103:		Line 103:

	== Summary Paragraph ==		== Summary Paragraph ==
		+	For [[Week 14\|Week 14]], I was assigned the task of making edits to [[Week 8\|Week 8]] and [[Week 10\|Week 10]] along with completing the remaining parts of [[Week 10\|Week 10]]. First, I selected the profile22 genelist and ranked the transcription factors using YEASTRACT and found that 49 of the transcription factors were significant. I further ranked those transcription factors from the lowest p-value to the highest p-value and chose the 20 lowest p-values. Two other transcription factors, HAP4 and GLN3 were including per instructions. These selected transcription factors listed above were put into the YEASTRACT database to generate a regulation matrix. This regulation matrix was then used to create a regulation network from GRNsight to visualize the regulation between these transcription factors. This proves extremely helpful as a method of visualization the connections and ways that the transcription factors interact and regulate each other and even regulate themselves.

	== Deliverables ==		== Deliverables ==

@@ Line 102: / Line 102: @@
 #* Selected the menu item File > Open and selected "[[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved the screenshot as "[[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]"
-=== Summary Paragraph ===
+== Summary Paragraph ==
-===Deliverables===
+== Deliverables ==
 # YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
 # YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]

@@ Line 102: / Line 102: @@
 #* Selected the menu item File > Open and selected "[[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved the screenshot as "[[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]"
-==== Summary Paragraph ====
+=== Summary Paragraph ===
 ===Deliverables===

@@ Line 100: / Line 100: @@
 #* Named the worksheet containing your organized adjacency matrix "network" and Save.
 # Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
-#* Selected the menu item File > Open and selected "FILENAME" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved it as "FILENAME"
+#* Selected the menu item File > Open and selected "[[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved the screenshot as "[[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]"
-==== Summary of what you need to turn in for the individual Week 10 assignment ====
+==== Summary Paragraph ====
 ===Deliverables===

@@ Line 91: / Line 91: @@
 #** No transcription factors were deleted as all had at least "1" in a row or column for that transcription factor.
 #* Inserted a new worksheet into the Excel file, [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]. and named it "network".  Went back to the previous sheet and selected the entire matrix and copied it. Went to the new worksheet and clicked on the A1 cell in the upper left.  Selected "Paste special" from the "Home" tab.  In the window that appears, checked the box for "Transpose".
-#* Delete the "p" from each of the gene names in the columns.  Adjusted the case of the labels to make them all upper case.
+#* Deleted the "p" from each of the gene names in the columns.  Adjusted the case of the labels to make them all upper case.
 #* In cell A1, copied and pasted the text "rows genes affected/cols genes controlling".
 #* Alphabetization:
@@ Line 99: / Line 99: @@
 #** Sorted row 1 from left to right, excluding cell A1.  In the Custom Sort window, clicked on the options button and select sort left to right, excluding column 1.
 #* Named 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.
+# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
-#* Go to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
+#* Selected the menu item File > Open and selected "FILENAME" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved it as "FILENAME"
 ==== Summary of what you need to turn in for the individual Week 10 assignment ====

@@ Line 121: / Line 121: @@
 ==Acknowledgements==
-#Recieved help from both [[User:Dondi|Dondi]] and [[User:Kdahlquist|Dr. Dahlquist]] from feedback given and instructions given in class.
+# 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 10|Week 10]].
+# Copied and modified the instructions from [[Week 10|Week 10]].
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

@@ Line 129: / Line 129: @@
 ==References==
 #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.
 [[Category:Journal Entry]]

@@ Line 91: / Line 91: @@
 #** No transcription factors were deleted as all had at least "1" in a row or column for that transcription factor.
 #* Inserted a new worksheet into the Excel file, [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]. and named it "network".  Went back to the previous sheet and selected the entire matrix and copied it. Went to the new worksheet and clicked on the A1 cell in the upper left.  Selected "Paste special" from the "Home" tab.  In the window that appears, checked the box for "Transpose".
-#* 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.
+#* Delete the "p" from each of the gene names in the columns.  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, 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.
+#* Alphabetization:
-#** Select the area of the entire adjacency matrix.
+#** Selected the area of the entire adjacency matrix.
-#** Click the Data tab and click the custom sort button.
+#** Clicked the Data tab and clicked the custom sort button.
-#** Sort Column A alphabetically, being sure to exclude the header row.
+#** Sorted Column A alphabetically, excluding 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.
+#** Sorted row 1 from left to right, excluding cell A1.  In the Custom Sort window, clicked on the options button and select sort left to right, excluding column 1.
-#* Name the worksheet containing your organized adjacency matrix "network" and Save.
+#* Named 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.