Knguye66 Eyoung20 Week 15 - Revision history

Eyoung20: /* Conclusion */ added conclusion

2019-12-13T23:33:46Z

‎Conclusion: added conclusion

Eyoung20: added edits to methods

2019-12-13T23:21:49Z

added edits to methods

Eyoung20: /* Analyzing and Interpreting STEM Results */ made changes to the methods

2019-12-13T23:19:19Z

‎Analyzing and Interpreting STEM Results: made changes to the methods

Eyoung20: /* Purpose */ added more to the purpose

2019-12-13T23:17:14Z

‎Purpose: added more to the purpose

Knguye66: /* Conclusion */ edit

2019-12-13T22:43:30Z

‎Conclusion: edit

Knguye66: /* Data and files */ edit and add

2019-12-13T21:12:43Z

‎Data and files: edit and add

Eyoung20: /* Data and files */ added data file

2019-12-13T20:18:19Z

‎Data and files: added data file

Eyoung20: /* Methods and Results: Progress */

2019-12-13T19:44:44Z

‎Methods and Results: Progress

Eyoung20: /* production_rates sheet */

2019-12-13T19:37:32Z

‎production_rates sheet

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Eyoung20: /* Data and files */

2019-12-08T23:57:26Z

‎Data and files

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 == Conclusion ==
   In a crunch for time, the methods are mixed between present and past tense.
 ==Data and files==

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 #**** P-value:0.000006235
 # For the mathematical model that we will build, we need to define a ''gene regulatory network'' of transcription factors that regulate other transcription factors.  We can use YEASTRACT to assist us with creating the network.  We want to generate a network with approximately 15-20 transcription factors in it.
 #* Go back to the YEASTRACT database and follow the link to ''[http://www.yeastract.com/formregmatrix.php Generate Regulation Matrix]''.
 #* Copy and paste the list of transcription factors you identified (plus HAP4, GLN3, and CIN5) into both the "Transcription factors" field and the "Target ORF/Genes" field.

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 #* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table".  For each of the profiles, click on the "Profile Gene Table" button to see the list of genes 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#_genelist.txt", where you replace the number symbol with the actual profile number.
 #** Upload these files to the wiki and link to them on your individual journal page.  (Note that it will be easier to [[Week_4#Compressing_and_Decompressing_Files_with_7-Zip | zip all the files together]] and upload them as one file).
-#* For each of the significant profiles, click 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!
+#* For each of the significant profiles, click 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". At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
 #** Upload these files to the wiki and link to them on your individual journal page.  (Note that it will be easier to [[Week_4#Compressing_and_Decompressing_Files_with_7-Zip | zip all the files together]] and upload them as one file).

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 == Purpose ==
-The purpose of this assignment is to record our progress towards the [[FunGals]] group [[Final_Project_Deliverables | deliverables]] as the [[Data_Analysis | Data Analysts]] for this week and the future weeks to come. The purpose of week 12 specifically was to download and adapt the data to the formatting we need for analysis. Then to begin the analysis with ANOVA and preparations for STEM.
+The purpose of this assignment is to record our progress towards the [[FunGals]] group [[Final_Project_Deliverables | deliverables]] as the [[Data_Analysis | Data Analysts]] for this week and the future weeks to come. The purpose of week 12 specifically was to download and adapt the data to the formatting we need for analysis. Then to begin the analysis with ANOVA and preparations for STEM.Once STEM has been prepare and run then we will take the information to create profiles, to analyses in YEASTRACT, and then Visualize those results in GRNsight. Then using those results an the Database create a GRNmap input workbook, and run it through GRNmap to get the final weighted network visualized in GRNsight.
 == Methods and Results: Progress ==

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 == Conclusion ==
-The first stage of our group's project was completed via referencing [[Week 8]] and using Microsoft Excel to complete the tasks. The excel file will be located in the [[FunGals]] page for viewing and download. We were able to successfully complete the ANOVA analysis and correct found mistakes. We were able to complete a sanity check with results showing. For the sanity check the unadjusted p- values showed 37.2% of the genes had a p<0.05, 18.16% had a p<0.01, 5.04% have p<0.001, and 0.87% have p<0.0001. The sanity check for the Bonferroni-corrected p-value 0.11% of the genes have p<0.05. For the sanity check on the Benjamini and Hochberg-corrected p-value 16.36% go the genes had a p <0.05. Finally we were able to prepare the Data to run STEM in the next step of working on this project.
+ In a crunch for time, the methods are mixed between present and past tense.
 ==Data and files==

← Older revision		Revision as of 21:12, 13 December 2019
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	[[media:Queries_Run_for_the_Red_Profile_in_Acess_Database.pptx\|Query Designs Red Profile]]		[[media:Queries_Run_for_the_Red_Profile_in_Acess_Database.pptx\|Query Designs Red Profile]]
		+
		+	[[media:Green Query Acess.pptx\|Query Designs Green Profile]]

	== Acknowledgements ==		== Acknowledgements ==

← Older revision		Revision as of 20:18, 13 December 2019
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	[[media:Data_for_FunGals.pptx\|FunGals Data on Powerpoint]]		[[media:Data_for_FunGals.pptx\|FunGals Data on Powerpoint]]
		+
		+	[[media:Queries_Run_for_the_Red_Profile_in_Acess_Database.pptx\|Query Designs Red Profile]]

	== Acknowledgements ==		== Acknowledgements ==

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 ** The left-most column should contain the header "id" and list the standard names for the genes in the model in the same order as in the other sheets.
 ** The second column should have the header "threshold_b" and should contain the initial guesses, we are going to use all 0.
 == Conclusion ==

← Older revision		Revision as of 23:57, 8 December 2019
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	[[Media:GRN_Model_Red_from_Matlab.zip \| Output Workbook & GRNModel from MatLab for Red profile (.zip)]]		[[Media:GRN_Model_Red_from_Matlab.zip \| Output Workbook & GRNModel from MatLab for Red profile (.zip)]]
−
−	~~[[File:Green_GRNsight_output.png\|500px\|thumb\|center\| Output GRNsight for Green profile]]~~

	[[media:Data_for_FunGals.pptx\|FunGals Data on Powerpoint]]		[[media:Data_for_FunGals.pptx\|FunGals Data on Powerpoint]]