Mavila9 Week 9 - Revision history

Mavila9: /* References */

2019-10-31T06:25:32Z

‎References

Mavila9: /* References */ websites

2019-10-31T06:24:09Z

‎References: websites

Mavila9: /* Conclusion */ conclusion summary

2019-10-31T05:21:16Z

‎Conclusion: conclusion summary

Mavila9: /* Methods & Results */

2019-10-31T05:08:02Z

‎Methods & Results

Mavila9: /* Data */

2019-10-31T04:58:00Z

‎Data

Mavila9: /* Part 2 */

2019-10-29T22:56:33Z

‎Part 2

Mavila9: /* Conclusion */

2019-10-29T22:49:19Z

‎Conclusion

Mavila9: /* Conclusion */ geneontology

2019-10-29T22:40:25Z

‎Conclusion: geneontology

Mavila9: /* Data */

2019-10-29T22:32:34Z

‎Data

Mavila9: /* Data */

2019-10-29T22:30:58Z

‎Data

@@ Line 65: / Line 65: @@
 GRNsight. Retrieved October 29, 2019, from https://dondi.github.io/GRNsight/ .
 Week 9. Retrieved October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9 .
 YEASTRACT. Retrieved October 29, 2019, from http://www.yeastract.com/formregmatrix.php .

← Older revision		Revision as of 06:24, 31 October 2019
Line 63:		Line 63:

	== References ==		== References ==
		+
		+	GRNsight. Retrieved October 29, 2019, from https://dondi.github.io/GRNsight/ .

	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 .
		+
		+	YEASTRACT. Retrieved October 29, 2019, from http://www.yeastract.com/formregmatrix.php .

@@ Line 54: / Line 54: @@
 == Conclusion ==
-===Part 1===
-#Why did you select this profile? In other words, why was it interesting to you?
+In this section of the investigation, the gene expression profile 9 from the STEM results were selected to further analyze. The profile 9 genes showed initial decreases then increase back to normal expression over time in response to cold shock. It is thought that the profile 9 genes share the same expression pattern because they are regulated by the same transcription factors. [http://www.yeastract.com/formregmatrix.php YEASTRACT] is used to prepare the profile 9 data to form a gene regulatory network of transcription factors using [https://dondi.github.io/GRNsight/ GRNsight]. This network can be used to find association between regulation of genes in response to cold shock.
 == Acknowledgements ==

← Older revision		Revision as of 05:08, 31 October 2019
Line 8:		Line 8:

	Steps were followed according to [[Week 9 \| Week 9 Assignment page]].		Steps were followed according to [[Week 9 \| Week 9 Assignment page]].
		+
		+	===Part 1===
		+	#Why did you select this profile? In other words, why was it interesting to you?
		+	#* I chose this profile because it was statistically significant and included a decrease in expression.
		+	#How many genes belong to this profile?
		+	#* 200 genes are assigned to this profile.
		+	#How many genes were expected to belong to this profile?
		+	#* 60.3 genes were expected to belong to this profile.
		+	#What is the p value for the enrichment of genes in this profile?
		+	#* 3.1x10(^-48) is the p-value for the enrichment of genes in this profile.
		+	#How many GO terms are associated with this profile at p < 0.05?
		+	#* 28 GO terms are associated with this profile at p < 0.05.
		+	#How many GO terms are associated with this profile with a corrected p value < 0.05?
		+	#* 3 GO terms are associated with this profile at p < 0.05.
		+	#GO:0000139 definition:
		+	#* Golgi membrane
		+	#GO:0006888 definition:
		+	#* endoplasmic reticulum to Golgi vesicle-mediated transport
		+	#GO:0015031 definition:
		+	#*protein transport
		+	#GO:0005794 definition:
		+	#* Golgi apparatus
		+	#GO:0002181 definition:
		+	#* cytoplasmic translation
		+	# GO:0005737 definition:
		+	#* cytoplasm
		+	===Part 2===
		+	#How many transcription factors are green or "significant"?
		+	#* 11 transcription factors are green
		+	#Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
		+	#* CIN5 is 16% in user set, 1.47% in YEASTRACT, and has a p-value of 0.999998732.
		+	#* GLN3 is 31.5% in user set, 2.6% in YEASTRACT, and has a p-value of 0.729017447.

	== Data ==		== Data ==

@@ Line 11: / Line 11: @@
 == Data ==
-[[media:Genelist mavila9.zip | genelist]]
+[[media:Wt microarray-data mavila9.xlsx | Microarray data .xlsx]]
-[[media:GOlist mavila9.zip | GOlist]]
+[[media:Wt profile9 RegulationMatrix YEASTRACT mavila9.xlsx | YEASTRACT .xlsx]]
-[[media:BIOL367 F19 microarray-data wt mavila9.xlsx | Microarray data]]
+[[media:Genelist mavila9.zip | genelist .xlsx]]
-[[media:BIOL367 F19 sample p-value slide mavila9.zip | STEM results]]
+[[media:GOlist mavila9.zip | GOlist .xlsx]]
 == Conclusion ==

@@ Line 48: / Line 48: @@
 #How many transcription factors are green or "significant"?
 #* 11 transcription factors are green
 == Acknowledgements ==

@@ Line 20: / Line 20: @@
 == Conclusion ==
+===Part 1===
 #Why did you select this profile? In other words, why was it interesting to you?
 #* I chose this profile because it was statistically significant and included a decrease in expression.
@@ Line 45: / Line 45: @@
 # GO:0005737 definition:
 #* cytoplasm
 == Acknowledgements ==

@@ Line 33: / Line 33: @@
 #How many GO terms are associated with this profile with a corrected p value < 0.05?
 #* 3 GO terms are associated with this profile at p < 0.05.
 == Acknowledgements ==

@@ Line 10: / Line 10: @@
 == Data ==
 [[media:Genelist mavila9.zip]]
 [[media:GOlist mavila9.zip]]
 [[media:BIOL367 F19 microarray-data wt mavila9.xlsx]]
 [[media:BIOL367 F19 sample p-value slide mavila9.zip]]