Cdomin12 Week 9 - Revision history

Cdomin12: /* References */ added grnsight and yeastract

2019-10-31T05:47:11Z

‎References: added grnsight and yeastract

2019-10-30T20:16:37Z

‎References: added sig

2019-10-30T20:16:25Z

‎Conclusion: added response

2019-10-30T20:10:05Z

‎Purpose: add

2019-10-30T20:04:15Z

deleted * ‎How many GO terms are associated with this profile with a corrected p value < 0.05?

2019-10-30T20:03:43Z

‎How many GO terms are associated with this profile with a corrected p value < 0.05?: added #

2019-10-30T20:03:06Z

‎How many GO terms are associated with this profile with a corrected p value < 0.05?: deleted #

2019-10-30T20:02:15Z

‎Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".: add explaination for TF

2019-10-30T20:00:31Z

‎How many GO terms are associated with this profile with a corrected p value < 0.05?: change numbers

2019-10-30T20:00:05Z

‎How many GO terms are associated with this profile with a corrected p value < 0.05?

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 ==References==
 *GeneOntology. Retrieved October 28, 2019 from http://geneontology.org
 *Week 9. Retrieved October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
 [[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 13:16, 30 October 2019 (PDT)

← Older revision		Revision as of 20:16, 30 October 2019
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	*GeneOntology. Retrieved October 28, 2019 from http://geneontology.org		*GeneOntology. Retrieved October 28, 2019 from http://geneontology.org
	*Week 9. Retrieved October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9		*Week 9. Retrieved October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
		+
		+	[[User:Cdomin12\|Cdomin12]] ([[User talk:Cdomin12\|talk]]) 13:16, 30 October 2019 (PDT)

← Older revision		Revision as of 20:16, 30 October 2019
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	==Conclusion==		==Conclusion==
		+	I only had 2 significant transcription factors when I ran the data through YEASTRACT. I chose the top 13 transcription factors to analyze with GRNsight, which include Gln3 and added CIN5 and HAP4 for a total of 15 transcription factors. GRNsight graph revealed only a node of HMO1 connected to itself. This gene regulatory network is interesting as there were no other connecting nodes to one another. This would show that HMO1 self regulates and no other transcription factors are shown to regulate others in my dataset.

	==Acknowledgments==		==Acknowledgments==

← Older revision		Revision as of 20:10, 30 October 2019
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	==Purpose==		==Purpose==
		+	To further analysis and understand the importance of significant transcription factors and their role in gene expression during and after cold shock.

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

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 ##*Selected the top 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
-##*** Note whether the same GO terms are showing up in multiple clusters.
+##**Note whether the same GO terms are showing up in multiple clusters.
 ##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].  In your research presentation, you will discuss the biological interpretation of these GO terms.  In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?  Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?'''''
 ##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].

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 #* Selected from this list of "significant" transcription factors, which ones you will use to run the model. Add GLN3, HAP4, and CIN5 .  Explained in your electronic notebook how you decided on which transcription factors to include.  Record the list and your justification in your electronic lab notebook.  Each group member will select a different network (they can have some overlapping transcription factors, but some should also be different).
 #* Go back to the YEASTRACT database and follow the link to ''[http://www.yeastract.com/formregmatrix.php Generate Regulation Matrix]''.
 #* Copied and pasted the list of transcription factors you identified (plus HAP4, GLN3, and CIN5) into both the "Transcription factors" field and the "Target ORF/Genes" field.