Hivanson Week 10 - Revision history

Hivanson: /* Conclusion */ conclusion complete

2024-04-04T06:11:46Z

‎Conclusion: conclusion complete

2024-04-04T06:07:22Z

‎Conclusion: conclusion save

2024-04-04T05:46:13Z

‎Clustering and GO Term Enrichment with stem: why 22?

2024-04-04T05:03:46Z

‎Creating and Visualizing Your Gene Regulatory Network with GRNsight: a note

2024-04-04T05:01:00Z

‎References: all refs

2024-04-04T04:58:59Z

‎References: week 10 source

2024-04-04T04:57:38Z

‎References: sgd source

2024-04-04T04:35:34Z

‎Clustering and GO Term Enrichment with stem: dcin5 explanation?

2024-04-04T04:16:15Z

‎Purpose: purpose done

2024-04-04T04:13:44Z

‎Acknowledgments: acknowledgements section

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 ===Conclusion===
-The analysis of the ∆CIN5 DNA microarray set revealed that profile 22 had significantly more genes than predicted that followed the trend of spiking in upregulation at the 90-minute time mark of cold shock. The genes found in this profile are associated with cell stress responses, as well as various cell parts and organelles.
+The analysis of the ∆CIN5 DNA microarray set revealed that profile 22 had significantly more genes than predicted that followed the trend of spiking in upregulation at the 90-minute time mark of cold shock. The genes found in this profile are associated with cell stress responses, as well as various cell parts and organelles. A gene regulatory network was formed of the most significantly affected (by cold shock) transcription factors in profile 22, and CIN5 did not connect into the network with the most significant transcription factors. Further analysis will be performed after my workbook is run through GRNmap modeling software.
 ===Acknowledgments===

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 ===Conclusion===
 ===Acknowledgments===
 I worked on this assignment in class on 3/28/2024 and 4/2/2024 under the guidance of [[User:Kdahlquist|Dr. Kam Dahlquist]]. All procedure was edited from [https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10 LMU Bio DB Week 10].

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 ## I selected profile 22 for further intepretation of the data.
 ##*'''Why did you select this profile? In other words, why was it interesting to you?'''
-##**I selected profile 22 because the overall trend of a spike only at 90 minutes is different from the rest of the profiles' trends.
+##**I selected profile 22 because the overall trend of a spike only at 90 minutes is different from the rest of the profiles' trends. Further, it had the second highest number of genes belonging to it out of all significant profiles.
 ##*'''How many genes belong to this profile?'''
 ##**179 genes

← Older revision		Revision as of 05:03, 4 April 2024
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	[[Image:GRN_dCIN5_prof22_hivanson_final.png\|750px]]		[[Image:GRN_dCIN5_prof22_hivanson_final.png\|750px]]
		+	Note: None of the transcriptions I tried would connect a node to CIN5.

	====Creating the GRNmap Input Workbook====		====Creating the GRNmap Input Workbook====

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 ===References===
 *Help:Table. (2024). In Wikipedia. Retrieved March 25, 2024, from https://en.wikipedia.org/w/index.php?title=Help:Table&oldid=1213890372
 *Saccharomyces Genome Database. (n.d.) CIN5 / YOR028C Overview. Retrieved April 3, 2024, from https://www.yeastgenome.org/locus/S000005554
-*LMU BioDB 2024. (2024). Week 10. Retrieved April 3, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
+*S.cerevisiae—Yeastract. (n.d.). Retrieved April 3, 2024, from http://www.yeastract.com/
 {{Template:Hivanson}}

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 ##***The genes that are associated with these GO terms include stress responses, like <code>cellular response to oxidative stress</code>, and its related terms that I excluded from the above table due to similarity. This makes sense as cold shock is considered a stressor. Additionally, various cellular structure components are associated with these GO terms, such as <code>cytoplasm</code>, <code>cytoskeleton</code>, and <code>fungal-type vacuole</code> which all may need to have regulated rigidity, fluidity or some other physical characteristics at lower temperatures.
 ##**'''Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)'''
-##***I want to compare our results to that of the wildtype. I don't understand completely what effects the CIN5 deletion should have, or what this does to the yeast. I tried reading the SGD description of CIN5. Will clarify with Dr. Dahlquist.
+##***I want to compare our results to that of the wildtype. The [https://www.yeastgenome.org/locus/S000005554 SGD description of CIN5] says it is <code>nuclearly localized under oxidative stress</code>, so perhaps with the deletion of CIN5 transcription factor, oxidative stress, and possibly other stress responses would be unable to occur.
 {| class="wikitable"

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 ===Purpose===
-We are analyzing a DNA microarray dataset, involving clustering and analysis of gene regulatory networks using GRNsight. The DNA microarray dataset is of the ''S. cerevisiae'' genome's cold shock response in a ∆CIN5 strain. This analysis will enable us to understand how
+We are analyzing a DNA microarray dataset, involving clustering and analysis of gene regulatory networks using GRNsight. The DNA microarray dataset is of the ''S. cerevisiae'' genome's cold shock response in a ∆CIN5 strain. This analysis will enable us to understand the role of the transcription factor CIN5's role in the cold shock response in ''S. cerevisiae''.
 ===Methods/Results===