Jcowan4 Journal Week 9 - Revision history

Jcowan4: /* Data and Files */ added correct sight map

2019-10-31T22:35:58Z

‎Data and Files: added correct sight map

Jcowan4: /* Conclusion */ ehh conclusion

2019-10-31T06:57:57Z

‎Conclusion: ehh conclusion

Jcowan4: /* Data and Files */ added error message

2019-10-31T06:52:09Z

‎Data and Files: added error message

Jcowan4: /* Data and Files */ added power point

2019-10-31T06:49:38Z

‎Data and Files: added power point

Jcowan4: /* Data and Files */ added matersheet

2019-10-31T06:48:28Z

‎Data and Files: added matersheet

Jcowan4: /* Data and Files */ added matrix

2019-10-31T06:46:22Z

‎Data and Files: added matrix

Jcowan4: /* Answers */ answered questions

2019-10-31T06:24:12Z

‎Answers: answered questions

Jcowan4: /* Answers */ editied answers

2019-10-31T06:16:15Z

‎Answers: editied answers

Jcowan4: /* Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes */ ansered a question

2019-10-31T06:15:26Z

‎Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: ansered a question

Jcowan4: /* Methods/Results */ added more procedure

2019-10-31T06:07:45Z

‎Methods/Results: added more procedure

← Older revision		Revision as of 22:35, 31 October 2019
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	[[Media:Error_File.PNG \| Error Message in place of REQ. photo]]		[[Media:Error_File.PNG \| Error Message in place of REQ. photo]]
		+
		+	[[Media:GRN_Sight_Map.PNG \| SightMap]]

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 06:57, 31 October 2019
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	==Conclusion==		==Conclusion==
		+
		+	In conclusion, my group was able to analyze each individual gene and be able to organize the data, figure out how to use Gene Ontology, how to understand data and figures involving data arrays.
		+
	==References==		==References==

← Older revision		Revision as of 06:52, 31 October 2019
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	[[Media:BIOL367_F19_Stem_Slides_Cowan.pptx \| Presentation Slides]]		[[Media:BIOL367_F19_Stem_Slides_Cowan.pptx \| Presentation Slides]]
		+
		+	[[Media:Error_File.PNG \| Error Message in place of REQ. photo]]

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 06:49, 31 October 2019
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	[[Media:BIOL367_F19_microarray-data_wt_Cowan.xlsx \| Updated Master Sheet]]		[[Media:BIOL367_F19_microarray-data_wt_Cowan.xlsx \| Updated Master Sheet]]
		+
		+	[[Media:BIOL367_F19_Stem_Slides_Cowan.pptx \| Presentation Slides]]

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 06:48, 31 October 2019
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	[[Media:RegulationMatrix_Documented_20191031_631_365213870_Cowan.xlsx \| Matrix]]		[[Media:RegulationMatrix_Documented_20191031_631_365213870_Cowan.xlsx \| Matrix]]
		+
		+	[[Media:BIOL367_F19_microarray-data_wt_Cowan.xlsx \| Updated Master Sheet]]

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 06:46, 31 October 2019
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	[[Media:Cowan_wt_GOfiles.zip \| Gene GO Files]]		[[Media:Cowan_wt_GOfiles.zip \| Gene GO Files]]
		+
		+	[[Media:RegulationMatrix_Documented_20191031_631_365213870_Cowan.xlsx \| Matrix]]

	==Conclusion==		==Conclusion==

@@ Line 90: / Line 90: @@
 *'''''How many GO terms are associated with this profile with a corrected p value < 0.05?''''' 4 genes
 *'''''How many transcription factors are green or "significant"?''''' 52 are significant
 ==Data and Files==

@@ Line 44: / Line 44: @@
 #* 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"?'''''
+#* 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"?''''' 52 are 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.'''''

← Older revision		Revision as of 06:07, 31 October 2019
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	#** 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.