MSymond1 Week 10 - Revision history

Msymond1: finished references

2024-04-04T06:56:23Z

finished references

Msymond1: started references

2024-04-04T06:55:23Z

started references

Msymond1: added conclusion and acknowledgements

2024-04-04T06:54:02Z

added conclusion and acknowledgements

Msymond1: /* Answers to Questions */ deleted uneccesary section

2024-04-04T06:42:16Z

‎Answers to Questions: deleted uneccesary section

Msymond1: /* Data and Files */ added thumbnails

2024-04-04T06:41:41Z

‎Data and Files: added thumbnails

Msymond1: /* Data and Files */ added excel file

2024-04-04T06:40:16Z

‎Data and Files: added excel file

Msymond1: /* Data and Files */ removed photo

2024-04-04T06:36:19Z

‎Data and Files: removed photo

Msymond1: added data and files

2024-04-04T06:36:00Z

added data and files

Msymond1: /* Methods & Results */ added answers

2024-04-04T06:32:21Z

‎Methods & Results: added answers

Msymond1: /* Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes */ edited

2024-04-04T06:22:14Z

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

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 *Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., & Wanner, N. C. (2015). Parameter estimation for gene regulatory networks from microarray data: cold shock response in Saccharomyces cerevisiae. Bulletin of mathematical biology, 77(8), 1457-1492. DOI: 10.1007/s11538-015-0092-6
 *Ernst, J., & Bar-Joseph, Z. (2006). STEM: a tool for the analysis of short time series gene expression data. BMC bioinformatics, 7(1), 191. DOI: 10.1093/bioinformatics/bti1022
 *LMU BioDB 2024. (2024). Week 10. Retrieved April 2, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
 *Teixeira, M. C., Viana, R., Palma, M., Oliveira, J., Galocha, M., Mota, M. N., ... & Monteiro, P. T. (2023). YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Research, 51(D1), D785-D791. DOI: 10.1093/nar/gkac1041

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 I consulted my homework partner, Katie Miller, during class whenever I had a question. We did not communicate outside of class. I also consulted a few other classmates during class regarding this assignment. I also asked my professor several questions over the course of completing this assignment. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 23:54, 3 April 2024 (PDT)
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-[[media:Symonds_Week10_Profiles.zip]]
 ==Purpose==
 The purpose of this lab procedure was to continue the transcriptomic analysis phase of the class by using the GO clusters and and terms, and using GRN modeling and visualization to help understand the transcription factors involved in cold shock for yeast cells.
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 *[[media:Symonds_Miller_STEM_Presentation.pptx| Powerpoint Slides]]
 *[[media:Symonds_YEASTRACTresults.xlsx| YEASTRACT Results]]
-*[[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx| Yeastmine Excel File]]
+*[[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx| GRN Excel File]]
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 #** I Copied the entire content of the "network" sheet into the "network_weights" sheet.
 # '''''I saved and uploaded the Excel Workbook to the wiki and linked to it on the individual journal page.'''''
 ==Data and Files==

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 ==Data and Files==
 *[[media:Symonds_BIOL367_S24_microarray-data_wt_masterExcelFile.xlsx| Master Excel File]]
-*[[media:Symonds_Week10_Profiles.zip]]
+*[[media:Symonds_Week10_Profiles.zip| Profiles list]]
-*[[media: Symonds_week_10Golist.zip]]
+*[[media: Symonds_week_10Golist.zip| GO list]]
-*[[media:Symonds_Miller_STEM_Presentation.pptx]]
+*[[media:Symonds_Miller_STEM_Presentation.pptx| Powerpoint Slides]]
-*[[media:Symonds_YEASTRACTresults.xlsx]]
+*[[media:Symonds_YEASTRACTresults.xlsx| YEASTRACT Results]]
-*[[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx]]
+*[[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx| Yeastmine Excel File]]
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← Older revision		Revision as of 06:36, 4 April 2024
Line 147:		Line 147:
	#My GRNsight excel file [[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx]]		#My GRNsight excel file [[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx]]

		+	==Data and Files==
		+	*[[media:Symonds_Week10_Profiles.zip]]
		+	*[[media: Symonds_week_10Golist.zip]]
		+	*[[media:Symonds_Miller_STEM_Presentation.pptx]]
		+	*[[media:Symonds_YEASTRACTresults.xlsx]]
		+	*[[image:Symonds_4-3-24_GRN_(Yeastmine_-_SGD_2024-03-19;_19_genes,_41_edges).jpg\|500px\|thumb\|right\|]]
		+	*[[media:Symonds GRN (Yeastmine - SGD 2024-03-19; 19 genes, 41 edges) weighted.xlsx]]

	{{Template:MSymond1}}		{{Template:MSymond1}}

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 ##** Each member of the group reported on his or her own cluster in your research presentation. I chose terms that are the most significant, but that are also not too redundant.  For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
 ##*** I noted whether the same GO terms are showing up in multiple clusters.
-##**'''''I Looked up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].  In your journal entry, I discussed 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)?'''''
+##**'''''I Looked up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].'''''
 ##** To easily look up the definitions, I went to [http://geneontology.org http://geneontology.org].
 ##** I copied and pasted the GO ID (e.g. GO:0044848) into the search field on the left of the page.
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 ##***ribosomal small subunit assembly (GO:0000028): The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit.
 ##***transaminase activity (GO:0008483): Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity.
 ==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ====
 # I opened the gene list in Excel for the one of the significant profiles from the stem analysis that you chose to perform the GO analysis.  It was a cluster with a clear cold shock/recovery up/down or down/up pattern, and was one of the largest clusters.

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 #** I Copied by selecting and dragging down on the table.
 #** When pasting into Excel, I remembered to Paste special > Paste values.
-#** '''''I Uploaded the Excel file to the wiki and link to it in your electronic lab notebook.'''''
+#** '''''I Uploaded the Excel file to the wiki and linked to it in my electronic lab notebook.'''''
 #** '''''CIN5 is in the table, 39.00% is in user set, 3.39% is in scerevisiae, and the p-value is 0.005141327836732. GLN3 is also in the database, 34.00% is in the user set, 2.76% is in scerevisiae, and the p-value is 0.346793143826899.'''''