Simonwro120 Week 8 - Revision history

Simonwro120: finished assignment

2017-10-24T05:31:59Z

finished assignment

Simonwro120: Added to summary

2017-10-24T05:17:10Z

Added to summary

Simonwro120: added summary aspects

2017-10-24T04:37:47Z

added summary aspects

Simonwro120: syntax

2017-10-23T22:56:51Z

syntax

Simonwro120: aded my favorite gene info

2017-10-23T22:14:06Z

aded my favorite gene info

Simonwro120: added intro to Lab notebook

2017-10-23T09:39:01Z

added intro to Lab notebook

Simonwro120: added references/acknowledgements

2017-10-23T09:17:49Z

added references/acknowledgements

Simonwro120: added outline

2017-10-23T09:06:37Z

added outline

Simonwro120: syntax fix

2017-10-23T08:47:08Z

syntax fix

Simonwro120: added assignment steps

2017-10-23T08:29:39Z

added assignment steps

@@ Line 106: / Line 106: @@
 **SPT15 does seem to change gene expression due to cold shock.
 ==== Summary Paragraph ====
-*In our experiment, we studied data related to the gene expression of yeast genes when exposed to a "cold shock" treatment after deleting gene CIN5. The data analysis consisted of 5 time points (t-15, t-30, t-60, t-90, t-120) which all corresponded to different temperatures. the first temperatures reflect gene expression during the cold shock, the latter ones reflect the recovery. The data shows the ''"Log Fold Change"'' for the expression of each gene at each time point. Using this data, my group was able to calculate the p-values for each gene. Once we finished this, we found the Bonferroni corrected and B-H corrected p-values. After some analysis, my group partner and I decided that the Bonferroni correction gave the most strict results. We drew this conclusion because only 151 genes, which is 2% of the total, had a p-value of less than 0.05. This was compared to the B-H value after the adjustment. The values showed 1453 genes, which is 23% of the total, that had a p-value of less than 0.05. We then compared unadjusted p-values of 2290 genes, which is 37%of the total, who had p-values of less than 0.05, and then compared them to a gene which is known to change expression during cold shock: ''NSR1''. Our groups data shows that the NSR1 strain did happen to respond to cold shock of our strain (''dCIN5''). The gene SPT15 (my favorite gene) was also looked at. This gene did/did not appear to change expression in response to cold shock in the strain dCIN5.
+*In our experiment, we studied data related to the gene expression of yeast genes when exposed to a "cold shock" treatment after deleting gene CIN5. The data analysis consisted of 5 time points (t-15, t-30, t-60, t-90, t-120) which all corresponded to different temperatures. the first temperatures reflect gene expression during the cold shock, the latter ones reflect the recovery. The data shows the ''"Log Fold Change"'' for the expression of each gene at each time point. Using this data, my group was able to calculate the p-values for each gene. Once we finished this, we found the Bonferroni corrected and B-H corrected p-values. After some analysis, my group partner and I decided that the Bonferroni correction gave the most strict results. We drew this conclusion because only 151 genes, which is 2% of the total, had a p-value of less than 0.05. This was compared to the B-H value after the adjustment. The values showed 1453 genes, which is 23% of the total, that had a p-value of less than 0.05. We then compared unadjusted p-values of 2290 genes, which is 37%of the total, who had p-values of less than 0.05, and then compared them to a gene which is known to change expression during cold shock: ''NSR1''. Our groups data shows that the NSR1 strain did happen to respond to cold shock of our strain (''dCIN5''). My group member and I also looked at our genes. My favorite gene was SPT15 which did not seem to change gene expression in response to  the cold shock of our strain dCIN5.
 ==Acknowledgements==
@@ Line 112: / Line 112: @@
 #I'd also like to acknowledge the help both Dondi and Dr. Dahlquist gave in reference to navigating the excel software in an efficient way.
 #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
-[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 02:17, 23 October 2017 (PDT)
+Signature: [[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 02:17, 23 October 2017 (PDT)
 ==References==
 LMU BioDB 2017. (2017). Week 8. Retrieved October 19, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8]

@@ Line 106: / Line 106: @@
 **SPT15 does seem to change gene expression due to cold shock.
 ==== Summary Paragraph ====
-*In our experiment, we studied data related to the gene expression of yeast genes when exposed to a "cold shock" treatment after deleting gene CIN5. The data analysis consisted of 5 time points (t-15, t-30, t-60, t-90, t-120) which all corresponded to different temperatures. the first temperatures reflect gene expression during the cold shock, the latter ones reflect the recovery. The data shows the ''log fold change'' for the expression of each gene at each time point. Using this data, my group was able to calculate the p-values for each gene. Once we finished this, we found the Bonferroni corrected and B-H corrected p-values.
+*In our experiment, we studied data related to the gene expression of yeast genes when exposed to a "cold shock" treatment after deleting gene CIN5. The data analysis consisted of 5 time points (t-15, t-30, t-60, t-90, t-120) which all corresponded to different temperatures. the first temperatures reflect gene expression during the cold shock, the latter ones reflect the recovery. The data shows the ''"Log Fold Change"'' for the expression of each gene at each time point. Using this data, my group was able to calculate the p-values for each gene. Once we finished this, we found the Bonferroni corrected and B-H corrected p-values. After some analysis, my group partner and I decided that the Bonferroni correction gave the most strict results. We drew this conclusion because only 151 genes, which is 2% of the total, had a p-value of less than 0.05. This was compared to the B-H value after the adjustment. The values showed 1453 genes, which is 23% of the total, that had a p-value of less than 0.05. We then compared unadjusted p-values of 2290 genes, which is 37%of the total, who had p-values of less than 0.05, and then compared them to a gene which is known to change expression during cold shock: ''NSR1''. Our groups data shows that the NSR1 strain did happen to respond to cold shock of our strain (''dCIN5''). The gene SPT15 (my favorite gene) was also looked at. This gene did/did not appear to change expression in response to cold shock in the strain dCIN5.
 ==Acknowledgements==
 #I worked with my homework partner, [[User:Mbalducc|Mary Balducci]], on this assignment. We worked together in class and compared results for our formulas in Excel. We also spoke outside of class to compare what we were doing to make sure we were both getting the same results for the same strain, dCIN5. We met once more to double check our laboratory notebook modifications and discuss the summary paragraph the day before class.

@@ Line 2: / Line 2: @@
 *My group analyzed the strain dCIN5.
 *5871 replacements were made when I deleted the NAs from the spreadsheet.
-*[[Media:SW_Week8_xl.zip|Excel file with all worksheets needed for our gene, dCIN5]]
+*[[Media:SW_Week8_xl.zip|Excel file with all worksheets completed for our gene, dCIN5]]
 *[[Media:BIOL367_F17_dCIN5_p-value_slide_MB.pptx|Table for Comparing dCIN5 with WT]]
@@ Line 106: / Line 106: @@
 **SPT15 does seem to change gene expression due to cold shock.
 ==== Summary Paragraph ====
-*Write a summary paragraph that gives the conclusions from this week's analysis.
+*In our experiment, we studied data related to the gene expression of yeast genes when exposed to a "cold shock" treatment after deleting gene CIN5. The data analysis consisted of 5 time points (t-15, t-30, t-60, t-90, t-120) which all corresponded to different temperatures. the first temperatures reflect gene expression during the cold shock, the latter ones reflect the recovery. The data shows the ''log fold change'' for the expression of each gene at each time point. Using this data, my group was able to calculate the p-values for each gene. Once we finished this, we found the Bonferroni corrected and B-H corrected p-values.
 ==Acknowledgements==
 #I worked with my homework partner, [[User:Mbalducc|Mary Balducci]], on this assignment. We worked together in class and compared results for our formulas in Excel. We also spoke outside of class to compare what we were doing to make sure we were both getting the same results for the same strain, dCIN5. We met once more to double check our laboratory notebook modifications and discuss the summary paragraph the day before class.

@@ Line 1: / Line 1: @@
 =Microarray Assignment=
 *My group analyzed the strain dCIN5.
+*5871 replacements were made when I deleted the NAs from the spreadsheet.
-replacements were made when I deleted the NAs from the spreadsheet.
+*[[Media:SW_Week8_xl.zip|Excel file with all worksheets needed for our gene, dCIN5]]
+*[[Media:BIOL367_F17_dCIN5_p-value_slide_MB.pptx|Table for Comparing dCIN5 with WT]]
 ==Modified Assignment Steps/Electronic Notebook==

@@ Line 99: / Line 99: @@
 (My favorite gene info)
 **My favorite gene is SPT15
-**Unadjusted p-value:
+**Unadjusted p-value: 0.010214264
-**Bonferroni-corrected:
+**Bonferroni-corrected: 1
-**B-H corrected:
+**B-H corrected: 0.045511938
-**AvgLogFC t15:
+**AvgLogFC t15: 2.529437391
-**AvgLogFC t30:
+**AvgLogFC t30: 0.685719402
-**AvgLogFC t60:
+**AvgLogFC t60: 1.171702893
-**AvgLogFC t90:
+**AvgLogFC t90: -0.761564308
-**AvgLogFC t120:
+**AvgLogFC t120: -0.177686995
-**SPT15 does not/does appear to change due to heat shock.
+**SPT15 does seem to change gene expression due to cold shock.
 ==== Summary Paragraph ====
 *Write a summary paragraph that gives the conclusions from this week's analysis.

← Older revision		Revision as of 09:39, 23 October 2017
Line 1:		Line 1:
	=Microarray Assignment=		=Microarray Assignment=
		+	*My group analyzed the strain dCIN5.
		+
		+	5871 replacements were made when I deleted the NAs from the spreadsheet.
		+
		+	[[Media:SW_Week8_xl.zip\|Excel file with all worksheets needed for our gene, dCIN5]]
		+
		+	[[Media:BIOL367_F17_dCIN5_p-value_slide_MB.pptx\|Table for Comparing dCIN5 with WT]]

	==Modified Assignment Steps/Electronic Notebook==		==Modified Assignment Steps/Electronic Notebook==

← Older revision		Revision as of 09:06, 23 October 2017
Line 91:		Line 91:
	* For fun, find "your favorite gene" (from your web page) in the dataset. '''''What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?''''' Does your favorite gene change expression due to cold shock in this experiment?		* For fun, find "your favorite gene" (from your web page) in the dataset. '''''What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?''''' Does your favorite gene change expression due to cold shock in this experiment?
	(My favorite gene info)		(My favorite gene info)
		+	**My favorite gene is SPT15
		+	**Unadjusted p-value:
		+	**Bonferroni-corrected:
		+	**B-H corrected:
		+	**AvgLogFC t15:
		+	**AvgLogFC t30:
		+	**AvgLogFC t60:
		+	**AvgLogFC t90:
		+	**AvgLogFC t120:
		+	**SPT15 does not/does appear to change due to heat shock.

@@ Line 1: / Line 1: @@
 =Microarray Assignment=
 ==Assignment Steps==
 ===Statistical Data Analysis Part 1===
 # Create a new worksheet, naming it dCIN5_ANOVA".
@@ Line 90: / Line 91: @@
 * For fun, find "your favorite gene" (from your web page) in the dataset.  '''''What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values?  What is its average Log fold change at each of the timepoints in the experiment?'''''  Does your favorite gene change expression due to cold shock in this experiment?
 (My favorite gene info)