Mbalducc Week 14 - Revision history

Mbalducc: /* Files */ changed file

2017-12-05T23:52:29Z

‎Files: changed file

2017-12-05T23:48:27Z

‎Files: changed file

2017-12-05T23:31:11Z

‎Files: added file

2017-12-05T23:13:36Z

added my template

2017-12-01T01:53:58Z

‎Files

2017-12-01T01:53:11Z

added ppt file

2017-12-01T01:51:15Z

‎Visualizing Your Gene Regulatory Networks with GRNsight: typo

2017-12-01T01:50:33Z

‎References: added ref

2017-12-01T01:47:19Z

‎Acknowledgements: added link to guild

2017-12-01T01:42:04Z

‎Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: added notes

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 [[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 TF from YEASTRACT]]
-[[media:mbalducc_STEM.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]
+[[media:Mbalducc_STEMprofiles.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]
 [[media:Mbalducc_profile 22_RegulationMatrix_Documented_2017.xlsx]]

@@ Line 4: / Line 4: @@
 [[media:mbalducc_STEM.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]
-[[media:Mbalducc_RegulationMatrix_Documented_profile_22.xlsx]]
+[[media:Mbalducc_profile 22_RegulationMatrix_Documented_2017.xlsx]]
 ==Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes==

← Older revision		Revision as of 23:31, 5 December 2017
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	[[media:mbalducc_STEM.pdf\| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]		[[media:mbalducc_STEM.pdf\| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]
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		+	[[media:Mbalducc_RegulationMatrix_Documented_profile_22.xlsx]]

	==Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes==		==Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes==

← Older revision		Revision as of 23:13, 5 December 2017
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	YEASTRACT. Rank by TF. Retrieved November 30, 2017, from http://www.yeastract.com/formrankbytf.php		YEASTRACT. Rank by TF. Retrieved November 30, 2017, from http://www.yeastract.com/formrankbytf.php
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		+	{{template:mbalducc}}

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 [[media:Mbalducc_Profile_22_yeastract_data.xlsx| Excel Sheet of Profile #22 TF from YEASTRACT]]
-[[media:mbalducc_STEM.pdf]]
+[[media:mbalducc_STEM.pdf| PowerPoint of STEM profiles and Gene Regulatory Network from GRNsight]]
 ==Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes==

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 #** In the results window that appeared, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop.  I renamed this file with a meaningful name so that I could distinguish it from the other files I will generate.
-=== Visualizing Your Gene Regulatory Networks with GRNsight===
+=== Visualizing My Gene Regulatory Networks with GRNsight===
 # Followed these steps for each of the three files I generated:

← Older revision		Revision as of 01:50, 1 December 2017
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	==References==		==References==

−	LMU BioDB 2017. (2017). Week 10 ~~Retrieve~~ November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10	+	GRNsight. (2017). Home. Retrieved November 30, 2017 from http://dondi.github.io/GRNsight/
		+
		+	LMU BioDB 2017. (2017). Week 10 Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
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		+	YEASTRACT. Generate Regulation Matrix. Retrieved November 30, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
		+
		+	YEASTRACT. Rank by TF. Retrieved November 30, 2017, from http://www.yeastract.com/formrankbytf.php

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 ==Acknowledgements==
-I worked with the rest of the Data Analyst guild: [[User:Aporras1|Antonio Porras]], [[User:dbashour|Dina Bashoura]], and [[User:Emmatyrnauer|Emma Tyrnauer]] on this assignment. We spoke in class and created a group chat so we could ask each other questions and help each other as we worked on the project. I also used the instructions from the [[Week 10]] assignment. I edited the instructions slightly so they would be specific to the profile I chose and the procedure I followed.
+I worked with the rest of the  [[Data Analysis]] guild: [[User:Aporras1|Antonio Porras]], [[User:dbashour|Dina Bashoura]], and [[User:Emmatyrnauer|Emma Tyrnauer]] on this assignment. We spoke in class and created a group chat so we could ask each other questions and help each other as we worked on the project. I also used the instructions from the [[Week 10]] assignment. I edited the instructions slightly so they would be specific to the profile I chose and the procedure I followed.
 ==References==
 LMU BioDB 2017. (2017). Week 10 Retrieve November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10

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 # Next 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 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 select the regulation matrix .xlsx file that has the "network" worksheet in it that you formatted above.  GRNsight created a graph of the network, I screenshot this and added it to my PowerPoint.
 ==Acknowledgements==