Msamdars Week 9 - Revision history

Msamdars: /* Acknowledgments */ add sig

2019-10-31T02:03:44Z

‎Acknowledgments: add sig

Msamdars: /* Conclusion */ add conclusion

2019-10-31T02:03:32Z

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Msamdars: /* Data & Files */ add all files

2019-10-30T01:05:11Z

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Msamdars: /* Methods/Results */ add reasoning

2019-10-29T23:09:04Z

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Msamdars: /* Methods/Results */ add table

2019-10-29T23:02:38Z

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Msamdars: /* Methods/Results */ add more steps

2019-10-29T22:43:14Z

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Msamdars: /* Data & Files */ typo

2019-10-29T22:30:45Z

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2019-10-29T22:30:33Z

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Msamdars: /* Data & Files */ add proper files

2019-10-29T22:30:14Z

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2019-10-29T20:00:02Z

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← Older revision		Revision as of 02:03, 31 October 2019
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	Except for what is noted above, this individual journal entry was completed by me and not copied from another source.		Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
		+
		+	[[User:Msamdars\|Msamdars]] ([[User talk:Msamdars\|talk]]) 19:03, 30 October 2019 (PDT)

	==Other Links==		==Other Links==

← Older revision		Revision as of 02:03, 31 October 2019
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	==Conclusion==		==Conclusion==
		+	This week, we learned about using the STEM clustering software to identify clusters of genes in our deletion strain that have similar patterns of expression. This week, I chose to look at profile 9 of the CIN5 deletion strain yeast. This profile contains 78 genes with a p-value of 0.000016, a very significant value. I chose this pattern of gene expression because it shows a fairly regular pattern of expression - down-regulation, no change, and then up-regulation. The gene ontology terms have largely to do with DNA transcription and regulation of gene expression. This makes sense because a cell will likely decrease gene expression during environmental stress to focus on self-preservation.

	==Acknowledgments==		==Acknowledgments==

@@ Line 76: / Line 76: @@
 ==Data & Files==
-[[Media:BIOL367 F19 dCIN5 MS.xlsx|Updated Spreadsheet]]
+[[Media:BIOL367 F19 dCIN5 MS.xlsx|dCin5_MS Spreadsheet]]
-[[Media:Biol367 dcin5 ms stem spreadsheets.zip|STEM data]]
+[[Media:Biol367 dcin5 ms stem spreadsheets.zip|Gene & Go Lists .zip File]]
-[[Media:BIOL367 dCIN5 MS presentation.pptx|Slides]]
+[[Media:BIOL367 dCIN5 MS presentation.pptx|dCIN5_MS Powerpoint]]
 ==Conclusion==

@@ Line 70: / Line 70: @@
 </li>
 </ul>
+<li> Explain how you chose the transcription factors?</li>
 </ol>

@@ Line 3: / Line 3: @@
 ==Methods/Results==
-#Why did you select this profile? In other words, why was it interesting to you?
+<ol>
-#* I chose this profile because I saw the trend was very consistent. There was a clear trend of gene repression, followed by a period where gene expression was idled, followed by the last period of increased gene expression. I think that this is interesting because we can gain a clearer picture of what genes are activated initially, then repressed during cold shock.
+<li>Why did you select this profile? In other words, why was it interesting to you?</li>
-#How many genes belong to this profile?
+<ul>
-#* 78 genes belong to this profile.
+*I chose this profile because I saw the trend was very consistent. There was a clear trend of gene repression, followed by a period where gene expression was idled, followed by the last period of increased gene expression. I think that this is interesting because we can gain a clearer picture of what genes are activated initially, then repressed during cold shock.
-#How many genes were expected to belong to this profile?
+</ul>
-#* 47.1 genes were expected to belong to this profile.
+<li>How many genes belong to this profile?</li>
-#What is the p value for the enrichment of genes in this profile?
+<ul>
-##How many GO terms are associated with this profile at p < 0.05?
+*78 genes belong to this profile.
-##*There are 8 terms
+</ul>
-##How many GO terms are associated with this profile with a corrected p value < 0.05?
+<li>How many genes were expected to belong to this profile?</li>
-##*There are no terms.
+<ul>
-#* The p-value is 0.000016 (1.6 x 10^-5).
+*47.1 genes were expected to belong to this profile.
-#Look up the definitions for each of the terms at 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)?
+</ul>
-##GO:0003700
+<li>What is the p value for the enrichment of genes in this profile?</li>
-##*
+<ul>
-##GO:0045944
+*The p-value is 0.000016 (1.6 x 10^-5).
-##GO:0055114
+</ul>
-##GO:0016491
+<ol>
-##GO:0005783
+<li>How many GO terms are associated with this profile at p < 0.05?</li>
-##GO:0046872
+<ul>
-#How many transcription factors are green or "significant"?
+*There are 8 terms
-#* 3 are green or "significant".
+</ul>
-#Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
+<li>How many GO terms are associated with this profile with a corrected p value < 0.05?</li>
-#*
+<ul>
 {| class="wikitable"
 ! Gene
 ! % in user set
@@ Line 50: / Line 68: @@
 |-
 |}
 ==Data & Files==

@@ Line 25: / Line 25: @@
 ==Data & Files==
-[[Media:BIOL367 F19 dCIN5 MS.xlsx||Updated Spreadsheet]]
+[[Media:BIOL367 F19 dCIN5 MS.xlsx|Updated Spreadsheet]]
-[[Media:Biol367 dcin5 ms stem spreadsheets.zip||STEM data]]
-[[Media:BIOL367 dCIN5 MS presentation.pptx||Slides]]
+[[Media:Biol367 dcin5 ms stem spreadsheets.zipSTEM data]]
 ==Conclusion==

@@ Line 39: / Line 39: @@
 ==References==
 # LMU BioDB 2019. (2019). Week 9. Retrieved October 29, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
 # MediaWiki (2019). Category: Help. Retrieved October 29, 2019, from https://www.mediawiki.org/wiki/Category:Help