Dmadere Week 9 - Revision history

Dmadere: /* Data & Files */ uploaded screenshot

2019-10-31T22:39:58Z

‎Data & Files: uploaded screenshot

Dmadere: /* Viewing and Saving STEM Results */ added more instruction

2019-10-31T05:57:21Z

‎Viewing and Saving STEM Results: added more instruction

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Dmadere: /* Data & Files */ uploaded excel sheet

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← Older revision		Revision as of 22:39, 31 October 2019
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	[[Media:DM_RegulationMatrix_Documented_20191029_2248_1651802718.xlsx\|DM_dCIN5 Regulation Matrix]]		[[Media:DM_RegulationMatrix_Documented_20191029_2248_1651802718.xlsx\|DM_dCIN5 Regulation Matrix]]
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		+	[[File:DM_dCIN5_Gene_Regulatory_Network.PNG\|thumb\|DM_dCIN5 Gene Regulatory Network]]

	==Conclusion==		==Conclusion==

← Older revision		Revision as of 05:57, 31 October 2019
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	===Viewing and Saving STEM Results===		===Viewing and Saving STEM Results===
		+	# A new window opened called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
		+	#*Clicked on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", clicked on the radio button that says "Based on real time". Then closed the Interface Options window.
		+	#*Took a screenshot of this window (on a PC, simultaneously pressed the Alt and PrintScreen buttons to save the view in the active window to the clipboard) and pasted it into a PowerPoint presentation to save your figures.
		+	#Clicked on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
		+	#*Took a screenshot of each of the individual profile windows and save the images in PowerPoint presentation.
		+	#*At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, clicked on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, clicked on the "Save Table" button and save the file to your desktop. Made filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
		+	#*For each of the significant profiles, clicked on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!

	===Analyzing and Interpreting STEM Results===		===Analyzing and Interpreting STEM Results===

← Older revision		Revision as of 05:04, 31 October 2019
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	* S.cerevisiae. (n.d.). Retrieved October 30, 2019, from [http://www.yeastract.com/ http://www.yeastract.com/].		* S.cerevisiae. (n.d.). Retrieved October 30, 2019, from [http://www.yeastract.com/ http://www.yeastract.com/].
	* Short Time-series Expression Miner (STEM). (n.d.). Retrieved October 30, 2019, from [http://www.cs.cmu.edu/~jernst/stem/ http://www.cs.cmu.edu/~jernst/stem/].		* Short Time-series Expression Miner (STEM). (n.d.). Retrieved October 30, 2019, from [http://www.cs.cmu.edu/~jernst/stem/ http://www.cs.cmu.edu/~jernst/stem/].
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		+	{{Template:Dmadere}}

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 ==Acknowledgements==
 *I worked with my homework group [[User:Imacarae|Ivy]], [[User:Msamdars|Mihir]], and [[User:Eyoung20|Emma]] this week in class to complete this assignment. We talked about the assignment in class and texted about it as well if anyone needed help.
 *'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''
 *[[User:Dmadere|Dmadere]] ([[User talk:Dmadere|talk]]) 21:57, 30 October 2019 (PDT)

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 ==References==
-* Assignment Page
+* Gene Ontology Resource. (n.d.). Retrieved October 30, 2019, from [http://geneontology.org/ http://geneontology.org/].
-* Gene Ontology
+* Methodology as provided and edited from the assignment page, step-by-step instrutions, and assignment updates as listed by 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]
-* STEM
+* S.cerevisiae. (n.d.). Retrieved October 30, 2019, from [http://www.yeastract.com/ http://www.yeastract.com/].
-* YEASTRACT
+* Short Time-series Expression Miner (STEM). (n.d.). Retrieved October 30, 2019, from [http://www.cs.cmu.edu/~jernst/stem/ http://www.cs.cmu.edu/~jernst/stem/].

← Older revision		Revision as of 04:54, 31 October 2019
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	==Conclusion==		==Conclusion==
		+	The purpose of this experiment was to analyze dCIN5's gene profile and interpret the data given from the gene cluster. In doing so, different gene profiles were shown from dCIN5 in STEM to display the affect of the surrounding genes on the expression. From there, significant profiles were chosen to analyze further (Profile #22 for this example). The data was then analyzed further to determine which transcription factors regulate a cluster of genes. In doing so, the data was unable to be inputted into GRNsight, therefore, I was unable to see the gene regulatory networks.

	==Acknowledgements==		==Acknowledgements==

← Older revision		Revision as of 04:33, 31 October 2019
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	[[Media:DM_RegulationMatrix_Documented_20191029_2248_1651802718.xlsx\|DM_dCIN5 Regulation Matrix]]		[[Media:DM_RegulationMatrix_Documented_20191029_2248_1651802718.xlsx\|DM_dCIN5 Regulation Matrix]]
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		+	==Conclusion==

	==Acknowledgements==		==Acknowledgements==

← Older revision		Revision as of 04:32, 31 October 2019
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	==Purpose==		==Purpose==
		+	The purpose of this analysis was to get an understanding of how gene regulatory networks work corresponding to the Gene Profile 22, and to understand how to interpret gene clusters.

	==Methods/Results==		==Methods/Results==

← Older revision		Revision as of 04:25, 31 October 2019
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	[[Media:DM_dCIN5.xlsx\|DM_dCIN5 Master Excel Sheet]]		[[Media:DM_dCIN5.xlsx\|DM_dCIN5 Master Excel Sheet]]
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		+	[[Media:DM_RegulationMatrix_Documented_20191029_2248_1651802718.xlsx\|DM_dCIN5 Regulation Matrix]]

	==Acknowledgements==		==Acknowledgements==