Ymesfin Week 9 - Revision history

Ymesfin: /* Methods */ added definition of GO terms

2019-11-05T23:32:02Z

‎Methods: added definition of GO terms

Ymesfin: /* Results */ changed ppt

2019-11-01T01:33:54Z

‎Results: changed ppt

Ymesfin: /* Results */ changed file

2019-11-01T01:26:02Z

‎Results: changed file

Ymesfin: /* Conclusion */ added to conclusion

2019-10-31T00:44:58Z

‎Conclusion: added to conclusion

Ymesfin: /* Purpose */ added purpose

2019-10-31T00:36:57Z

‎Purpose: added purpose

Ymesfin: added references and signature

2019-10-31T00:31:50Z

added references and signature

Ymesfin: /* Methods */ changed format

2019-10-31T00:26:37Z

‎Methods: changed format

Ymesfin: /* Methods */ added methods

2019-10-31T00:25:26Z

‎Methods: added methods

Ymesfin: /* Data and Files */ deleted ppt

2019-10-31T00:08:29Z

‎Data and Files: deleted ppt

Ymesfin: /* Results */ added matrix

2019-10-31T00:07:54Z

‎Results: added matrix

@@ Line 47: / Line 47: @@
 ##**Only one term associated with this profile had a corrected p value < 0.05.
 ##The definitions of the top 6 terms with p-values <0.05 were searched on http://geneontology.org
 #Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes
 ## The gene list for Profile 48 was pasted onto [http://www.yeastract.com/index.php Yeastract] and ranked by TF

@@ Line 70: / Line 70: @@
 [[Media: Ymesfin_dHAP4_GOlist.zip| dHAP4 GO List]]
-[[Media: Ymesfin_dHAP4_slides.pptx| dHAP4 Slides]]
+[[Media: Ymesfin_dHAP4_slide.pdf| dHAP4 Slides]]
 [[Media: Ymesfin_dHAP4_regulation_matrix_network.xlsx| dHAP4 profile 48 Regulation Matrix]]

@@ Line 72: / Line 72: @@
 [[Media: Ymesfin_dHAP4_slides.pptx| dHAP4 Slides]]
-[[Media: Ymesfin_dHAP4_regulation_matrix.xlsx| dHAP4 profile 48 Regulation Matrix]]
+[[Media: Ymesfin_dHAP4_regulation_matrix_network.xlsx| dHAP4 profile 48 Regulation Matrix]]
 ==Conclusion==

← Older revision		Revision as of 00:44, 31 October 2019
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	==Conclusion==		==Conclusion==
		+	In this study, yeast cells (saccharomyces cerevisiae) were exposed to a cold shock to monitor how their gene expression levels related to environmental temperatures. The ANOVA suggest that approximately 40.1% of the collected data is statistically significant and had p values less than 0.05. However, given the large number of data entries used in the study, it is not unreasonable to assume that some of the significant results are due to chance, regardless of whether the p values were less than 0.05. Nonetheless, 4.5% of the data contained p values less than 0.0001, substantiating the significance of at least some of the data. Thus, the database suggests that there is a relationship between the expression levels of certain genes of saccharomyces cerevisiae and the cold shock treatments. Of the most significant stem profiles, Profile 48 was used for further analysis. GRNsight was used to analyze the relationship between the transcription factors associated with Profile 48. Most of the transcription factors were associated with one another creating a network.

	{{Template: ymesfin}}		{{Template: ymesfin}}

@@ Line 1: / Line 1: @@
 ==Purpose==
-The purpose of this assignment was to create a detailed electronic lab notebook to statistically analyze a DNA microarray dataset and to demonstrate our understanding of p-value cut-offs.
+The purpose of this assignment was to create a detailed electronic lab notebook to statistically analyze a DNA microarray dataset, demonstrate our understanding of p-value cut-offs, and display the relationships between the network of transcription factors in Saccharomyces cerevisiae.
 [[Week 7| Week 7 Assignment]]

@@ Line 86: / Line 86: @@
 Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
 ==References==
@@ Line 95: / Line 97: @@
 The Gene Ontology Resource. (2019). Retrieved October 26, 2019, from http://geneontology.org

@@ Line 48: / Line 48: @@
 ##The definitions of the top 6 terms with p-values <0.05 were searched on http://geneontology.org
 #Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes
-## The gene list for Profile 48 was pasted onto [[http://www.yeastract.com/index.php Yeastract]] and ranked by TF
+## The gene list for Profile 48 was pasted onto [http://www.yeastract.com/index.php Yeastract] and ranked by TF
 ##*How many transcription factors are green or "significant"?
 ##**9 are significant.
 ##*Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
 ##**CIN5: 16.47%, p value= 0.999999881503972;  GLN3: 35.29%, p value= 0.276481708725189;  HAP4: 14.51%, p value= 0.597297513212687
-##A regulation matrix was created from the top 15 transcription factors with the highest p-values and the transcription factors GLN3, HAP4, and CIN5 using the [[http://www.yeastract.com/formregmatrix.php Yeastract Gene Regulation Matrix]]
+##A regulation matrix was created from the top 15 transcription factors with the highest p-values and the transcription factors GLN3, HAP4, and CIN5 using the [http://www.yeastract.com/formregmatrix.php Yeastract Gene Regulation Matrix]
 #Visualizing Your Gene Regulatory Networks with GRNsight
 ##The regulation matrix was reformatted into an adjacency matrix
 ##The rows and columns of the adjacency matrix were sorted in alphabetical order
-##The data was visualized with a grid by uploading the adjacency matrix onto [[https://dondi.github.io/GRNsight/ GRNsight]]
+##The data was visualized with a grid by uploading the adjacency matrix onto [https://dondi.github.io/GRNsight/ GRNsight]
 ==Results==

← Older revision		Revision as of 00:08, 31 October 2019
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	[[Media: HW_ymesfin_data_dHAP4.txt\| dHAP4 Stem Data]]		[[Media: HW_ymesfin_data_dHAP4.txt\| dHAP4 Stem Data]]
−
−	~~[[Media: Ymesfin dHAP4 sanity check and stem.pptx\| dHAP4 P-Values and Stem Results]]~~

	[[Media: Ymesfin_dHAP4_genelist.zip\| dHAP4 Gene List]]		[[Media: Ymesfin_dHAP4_genelist.zip\| dHAP4 Gene List]]

← Older revision		Revision as of 00:07, 31 October 2019
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	[[Media: Ymesfin_dHAP4_slides.pptx\| dHAP4 Slides]]		[[Media: Ymesfin_dHAP4_slides.pptx\| dHAP4 Slides]]
		+
		+	[[Media: Ymesfin_dHAP4_regulation_matrix.xlsx\| dHAP4 profile 48 Regulation Matrix]]

	==Conclusion==		==Conclusion==