Data Analysts Week 14 - Revision history

Kmill104: /* Milestone 4 */

2024-05-03T19:12:29Z

‎Milestone 4

Kmill104: /* Milestone 4 */

2024-05-03T19:11:22Z

‎Milestone 4

Kmill104: /* Milestone 4 */ adding final steps

2024-05-03T18:58:13Z

‎Milestone 4: adding final steps

Kmill104: /* Milestone 4 */ adding link titles

2024-05-03T18:46:36Z

‎Milestone 4: adding link titles

Kmill104: /* Milestone 4 */ adding more steps

2024-05-03T18:45:37Z

‎Milestone 4: adding more steps

Kmill104: /* Continuing Milestone 3 */ adding cut off value

2024-05-03T18:36:26Z

‎Continuing Milestone 3: adding cut off value

Kmill104: /* Continuing Milestone 3 */ adding details

2024-05-03T18:34:32Z

‎Continuing Milestone 3: adding details

Kmill104: /* Acknowledgements */ adding signature

2024-05-03T02:15:14Z

‎Acknowledgements: adding signature

Kdahlquist: add correct template and categories

2024-05-01T20:31:34Z

add correct template and categories

Kdahlquist: add category

2024-04-30T16:24:54Z

add category

@@ Line 59: / Line 59: @@
 #*We ran YEASTRACT according to the protocol listed in Week 10 for clusters 41 and 7.
-#*We opened the gene list file in Excel for clusters 41 and 7.
+#*We opened the gene list file in Excel for cluster 41 and copied the list of gene IDs.
 #*We went to the YEASTRACT website at [http://www.yeastract.com/ YEASTRACT database], and clicked on "Rank by TF" in the left panel of the window. We pasted in our gene list for 41 into the box called "ORFs/Genes".
 #* We checked the box for ''Check for all TFs''.
 #* We accepted the defaults for the Regulations Filter (Documented, DNA binding or expression evidence)

@@ Line 62: / Line 62: @@
 #*We went to the YEASTRACT website at [http://www.yeastract.com/ YEASTRACT database], and clicked on "Rank by TF" in the left panel of the window. We pasted in our gene list for 41 into the box called "ORFs/Genes".
 #* We copied the list of gene IDs, which we then
 #* We checked the box for ''Check for all TFs''.
 #* We accepted the defaults for the Regulations Filter (Documented, DNA binding or expression evidence)

@@ Line 57: / Line 57: @@
 We made adjustments to the GO term analysis by using the GO enrichment tool at GeneOntology.org by going to [http://geneontology.org/ http://geneontology.org/] and then analyzing our clusters 41 and 7. We copied over each cluster's gene list from their txt. file converted to an Excel file into the "GO Enrichment Analysis" box, chose "Saccharomyces cerevisiae" from the drop-down menu, and then clicked "Launch". We then exported each table and saved as txt. files in BOX, linked here: [https://lmu.app.box.com/file/1512453796651 GO Terms 41], [https://lmu.app.box.com/file/1512450115120 GO Terms 7]
@@ Line 64: / Line 79: @@
 and 7 significant profiles
-Profile 41 grnsight:
+We then chose 23 transcription factors from profile 41, listed here.
 Rpn4
 Gcn4

← Older revision		Revision as of 18:46, 3 May 2024
Line 56:		Line 56:
	#We clicked on the "Profile Gene Table" button to see the list of genes belonging to each profile, and then downloaded these files to BOX.		#We clicked on the "Profile Gene Table" button to see the list of genes belonging to each profile, and then downloaded these files to BOX.

−	We made adjustments to the GO term analysis by using the GO enrichment tool at GeneOntology.org by going to [http://geneontology.org/ http://geneontology.org/] and then analyzing our clusters 41 and 7. We copied over each cluster's gene list from their txt. file converted to an Excel file into the "GO Enrichment Analysis" box, chose "Saccharomyces cerevisiae" from the drop-down menu, and then clicked "Launch". We then exported each table and saved as txt. files in BOX, linked here: [https://lmu.app.box.com/file/1512453796651], [https://lmu.app.box.com/file/1512450115120]	+	We made adjustments to the GO term analysis by using the GO enrichment tool at GeneOntology.org by going to [http://geneontology.org/ http://geneontology.org/] and then analyzing our clusters 41 and 7. We copied over each cluster's gene list from their txt. file converted to an Excel file into the "GO Enrichment Analysis" box, chose "Saccharomyces cerevisiae" from the drop-down menu, and then clicked "Launch". We then exported each table and saved as txt. files in BOX, linked here: [https://lmu.app.box.com/file/1512453796651 GO Terms 41], [https://lmu.app.box.com/file/1512450115120 GO Terms 7]

@@ Line 43: / Line 43: @@
 ===Milestone 4===
-#We inserted a new worksheet and named it "CHP_stem".
+#We inserted a new worksheet into our Excel workbook and named it "CHP_stem".
 #We selected all of the data from the "CHP_ANOVA" worksheet and Paste special > paste values into the "CHP_stem" worksheet.
 #"Master_Index" was renamed  to "SPOT". Column B named "ID" was renamed to "Gene Symbol". We deleted the column named "Standard_Name".
-#We filtered the data on the B-H corrected p value to be > 0.05.
+#We filtered the data on the B-H corrected p value to be > 0.0001.
 #We selected all of the rows except for the header row and deleted the rows by right-clicking and choosing "Delete Row" from the context menu. Then we undid this filter.
 #We deleted all of the data columns except for the Average Log Fold change columns for each timepoint.
@@ Line 53: / Line 53: @@
 #We saved this spreadsheet as Text (Tab-delimited) (*.txt).
 #We downloaded the stem.zip file and selected "Extract all" from the menu, creating a folder called stem.
-#We clicked on the "Profile GO Table" to see the list of Gene Ontology. We saved the file to our desktop.
+#We clicked on the "Profile GO Table" to see the list of Gene Ontology. We saved these files to our desktop.
-#We clicked on the "Profile Gene Table" button to see the list of genes belonging to the profile.
+#We clicked on the "Profile Gene Table" button to see the list of genes belonging to each profile, and then downloaded these files to BOX.
@@ Line 86: / Line 88: @@
 Rgm1
 Stp2
 ==Acknowledgements==

@@ Line 18: / Line 18: @@
 *CONTROL
 How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
+; 79%
 <.01
+; 68%
 <.001
+; 54%
 <.0001
+; 41%
 <.00001
-;
+; 28%
 *CHP
 How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
+; 61%
 <.01
+; 51%
 <.001
+; 40%
 <.0001
-; 30.55%
+; 31%
 <.00001
-; 22.91%
+; 22%
 ===Milestone 4===

← Older revision		Revision as of 02:15, 3 May 2024
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	[[User:Ckapla12\|Ckapla12]] ([[User talk:Ckapla12\|talk]]) 14:28, 23 April 2024 (PDT)		[[User:Ckapla12\|Ckapla12]] ([[User talk:Ckapla12\|talk]]) 14:28, 23 April 2024 (PDT)
		+
		+	[[User:Kmill104\|Kmill104]] ([[User talk:Kmill104\|talk]]) 19:15, 2 May 2024 (PDT)

	==References==		==References==

← Older revision		Revision as of 20:31, 1 May 2024
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	LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis		LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

−	{{Team Project}}	+	{{Yeast Beasts}}
		+	[[Category:Journal Entry]]
		+	[[Category:Team Project]]

← Older revision		Revision as of 16:24, 30 April 2024
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	LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis		LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
		+
		+	{{Team Project}}