Imacarae Week 9 - Revision history

Imacarae: /* Visualizing Your Gene Regulatory Networks with GRNsight */ added picture

2019-10-31T04:09:20Z

‎Visualizing Your Gene Regulatory Networks with GRNsight: added picture

Imacarae: /* Conclusion */ wrote paragraph

2019-10-31T04:03:52Z

‎Conclusion: wrote paragraph

Imacarae: /* References */ added grnsight

2019-10-31T03:45:42Z

‎References: added grnsight

Imacarae: /* Visualizing Your Gene Regulatory Networks with GRNsight */ edited tense

2019-10-31T03:43:00Z

‎Visualizing Your Gene Regulatory Networks with GRNsight: edited tense

Imacarae: /* Week 9 Procedure */ pasted procedure

2019-10-31T03:28:55Z

‎Week 9 Procedure: pasted procedure

Imacarae: /* Data and Files */ added reg matrix

2019-10-31T03:23:34Z

‎Data and Files: added reg matrix

Imacarae: /* Data and Files */ updated master excel link

2019-10-31T03:19:04Z

‎Data and Files: updated master excel link

Imacarae: /* Data and Files */ edited pptx

2019-10-31T03:17:16Z

‎Data and Files: edited pptx

Imacarae: /* Acknowledgments */ updated week 9 link

2019-10-31T00:30:00Z

‎Acknowledgments: updated week 9 link

Imacarae: /* Acknowledgments */ added statement and signed

2019-10-31T00:29:37Z

‎Acknowledgments: added statement and signed

@@ Line 209: / Line 209: @@
 #** I deleted 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), I transposed the matrix. I inserted a new worksheet into the Excel file and nameed it "network". I went back to the previous sheet and selected the entire matrix and copied it. I went back to my new worksheet and clicked on the A1 cell in the upper left, and selected "Paste special" from the "Home" tab. In the window that appears, I checked the box for "Transpose".  This pasted the 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.
-#* I matched all the genes together.
+#* I matched all the genes together. [[File:GRNsightgrid_Profile45_IM.PNG|500px|thumb]]
 #* 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.
 #** I select the area of the entire adjacency matrix.
 #** I clicked the Data tab and click the custom sort button.
 #** I sorted Column A alphabetically, being sure to exclude the header row.
 #** Then I sorted row 1 from left to right, excluding cell A1. In the Custom Sort window, I clicked on the options button and select sort left to right, excluding column 1.

@@ Line 231: / Line 231: @@
 ==Conclusion==
 ==Acknowledgments==
 *To [[User:Kdahlquist|Dr. Dahlquist]] for walking us through analyzing the data with Excel.

@@ Line 242: / Line 242: @@
 *Yeastract+. (2019). Retrieved October 30, 2019, from [http://www.yeastract.com/formregmatrix.php http://www.yeastract.com/formregmatrix.php].
 *LMU BioDB 2019. (2019). Week 9. Retrieved October 30, 2019, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9 https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9].
 [[Category:Journal Entry]]

@@ Line 202: / Line 202: @@
 #** In the results window that appears, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and save it to my T Drive. I rename this file to "RegulationMatrix_dCIN5_profile45".
 ==== 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.
+We analyzed the regulatory matrix files I generated above in Microsoft Excel and visualized 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.
+# First I properly formatted 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.
+#* 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. Then I 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, 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.
-#* Save this file in Microsoft Excel workbook format (.xlsx).
+#* I saved 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.-->
+#** I deleted 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 transposed the matrix. I inserted a new worksheet into the Excel file and nameed it "network". I went back to the previous sheet and selected the entire matrix and copied it. I went back to my new worksheet and clicked on the A1 cell in the upper left, and selected "Paste special" from the "Home" tab. In the window that appears, I checked the box for "Transpose".  This pasted the 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.
+#* I matched all the genes together.
-#* 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.
-#** Select the area of the entire adjacency matrix.
+#** I select the area of the entire adjacency matrix.
-#** Click the Data tab and click the custom sort button.
+#** I clicked the Data tab and click 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 select sort left to right, excluding column 1.
-#* Name the worksheet containing your organized adjacency matrix "network" and Save.
+#* I named the worksheet containing your organized adjacency matrix "network" and Saved.
-# Now we will visualize what these gene regulatory networks look like with the GRNsight software.
+# Now we visualized what these gene regulatory networks would 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.  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.
+#* I selected the menu item File > Open and select the regulation matrix .xlsx file that has the "network" worksheet in it that Iformatted above. I clicked 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 took a screenshot of the results. I pasted 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.
+#** I used this final version in your PowerPoint and subsequent modeling.
 ==Data and Files==

@@ Line 200: / Line 200: @@
 #* I used the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"
 #** I clicked the "Generate" button.
-#** In the results window that appears, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and save it to my T Drive. I rename this file
+#** In the results window that appears, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and save it to my T Drive. I rename this file to "RegulationMatrix_dCIN5_profile45".
 ==Data and Files==

@@ Line 208: / Line 208: @@
 *[[Media:BIOL367_F19_microarray-data_dCIN5_IM.txt|Txt File Used in STEM]]
 *[[Media:BIOL367_F19_microarray-data_dCIN5_IM.xlsx|(Updated) Master dCIN5 Excel Sheet]]
 ==Conclusion==

@@ Line 205: / Line 205: @@
 *[[Media:DCIN5_allprofiles_genelist_IM.zip|STEM Profiles: dCIN5 Gene List]]
 *[[Media:DCIN5_allprofiles_GOlist_IM.zip|STEM Profiles: dCIN5 GO List]]
-*[[Media:BIOL367_F19_sample_p-value_slide_IM.pptx|Updated PowerPoint]]
+*[[Media:BIOL367_F19_sample_p-value_slide_IM.pptx|(Updated) PowerPoint]]
 *[[Media:BIOL367_F19_microarray-data_dCIN5_IM.txt|Txt File Used in STEM]]
-*[[Media:BIOL367_F19_microarray-data_dCIN5_IM.xlsx|Master dCIN5 Excel Sheet]]
+*[[Media:BIOL367_F19_microarray-data_dCIN5_IM.xlsx|(Updated) Master dCIN5 Excel Sheet]]
 ==Conclusion==

@@ Line 212: / Line 212: @@
 ==Acknowledgments==
 *To [[User:Kdahlquist|Dr. Dahlquist]] for walking us through analyzing the data with Excel.
-*:-Procedural steps were copied from the [Week 9] assignment page and modified to fit the data.
+*:-Procedural steps were copied from the [[Week 9]] assignment page and modified to fit the data.
 *To my group members, [[User:Dmadere|DeLisa]], [[User:Msamdars|Mihir]], and [[User:Eyoung20|Emma]]. We met during class time to walk through the procedure and to delegate what profile we were going to do individually.
 *'''Except for what is noted above, this individual journal entry was completed by me and not copied from another source.'''