Cwong34 Week 10 - Revision history

Cwong34: Wrote summary

2017-11-04T21:15:46Z

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Cwong34: added references and acknowledgments

2017-11-04T21:01:07Z

added references and acknowledgments

Cwong34: Added files

2017-11-04T20:57:25Z

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Cwong34: Added to electronic notebook

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2017-11-04T20:05:16Z

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Cwong34: Edited electronic notebook

2017-11-04T19:54:18Z

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2017-11-02T23:03:49Z

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2017-10-31T22:02:32Z

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=Acknowledgments=

=References=

{{cwong34}}

[[Category: Journal Entry]]

← Older revision		Revision as of 21:15, 4 November 2017
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	===Summary===		===Summary===
		+	This week, we deleted all of the insignificant data (where the B-H corrected p-value was less than 0.05) from the spreadsheet, leaving 2643 genes. We reorganized the data so only the average log fold change columns remained with the labels of just their times (30m, 60m, etc.). We saved this spreadsheet as a text file, so we could upload it to the stem program and run it. In the stem results for dSWI4, 11 profiles came up as significant, which were profiles 11, 14, 23, 45, 47, 24, 44, 6, 5, 10, and 37. Seven of the significant profiles down-regulated after cold shock, whereas only four of them up-regulated. For profile #5, it down-regulated after cold shock, but returned to normal after 90 minutes. There are 73 genes assigned to this profile with 31.4 expected, and the p-value for this profile is 1.2E-10. There are 75 GO terms in this profile that have a p-value<0.05, and only 3 of them have a corrected p-value<0.05. Some of the gene ontology terms that are significant in this profile are "intracellular," "endomembrane system," "proteolysis," "Golgi aparatus part," "DNA recombination," and "protein localization."

	=Acknowledgments=		=Acknowledgments=

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 =Week 10 files=
 [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_CW.zip|dSWI4 Excel spreadsheet]]
 [[Media:dSWI4_STEM_results_CW.zip|dSWI4 STEM results]]
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 =Acknowledgments=
 =References=
+#LMU BioDB 2017. (2017). Week 10. Retrieved October 31, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 {{cwong34}}
 [[Category: Journal Entry]]

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-=STEM results=
+=Week 10 files=
 [[Media:dSWI4_STEM_results_CW.zip|dSWI4 STEM results]]
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 ===Summary===
 =Acknowledgments=

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 ##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
 ##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
 ===Summary===

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 ##* '''''What is the p value for the enrichment of genes in this profile?'''''  Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point.  This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
 ##** The p-value for the enrichment of genes in this profile is 1.2E-10.
-##* Open the GO list file you saved for this profile in Excel.  This list shows all of the Gene Ontology terms that are associated with genes that fit this profile.  Select the third row and then choose from the menu Data > Filter > Autofilter.  Filter on the "p-value" column to show only GO terms that have a p value of < 0.05.  '''''How many GO terms are associated with this profile at p < 0.05?'''''  The GO list also has a column called "Corrected p-value".  This correction is needed because the software has performed thousands of significance tests.  Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05.  '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
+##* Open the GO list file you saved for this profile in Excel.  This list shows all of the Gene Ontology terms that are associated with genes that fit this profile.  Select the third row and then choose from the menu Data > Filter > Autofilter.  Filter on the "p-value" column to show only GO terms that have a p value of < 0.05.  '''''How many GO terms are associated with this profile at p < 0.05?''''' - '''75 GO terms'''  The GO list also has a column called "Corrected p-value".  This correction is needed because the software has performed thousands of significance tests.  Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05.  '''''How many GO terms are associated with this profile with a corrected p value < 0.05?''''' - '''3 GO terms'''
 ##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
 ##** Each member of the group will be reporting on his or her own cluster in your presentation next week.  You should take care to choose terms that are the most significant, but that are also not too redundant.  For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.

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 ## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data.  I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints.  '''''Each member of your group should choose a different profile.'''''  Answer the following:
 ##* '''''Why did you select this profile?  In other words, why was it interesting to you?'''''
 ##* '''''How many genes belong to this profile?'''''
 ##* '''''How many genes were expected to belong to this profile?'''''
 ##* '''''What is the p value for the enrichment of genes in this profile?'''''  Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point.  This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
 ##* Open the GO list file you saved for this profile in Excel.  This list shows all of the Gene Ontology terms that are associated with genes that fit this profile.  Select the third row and then choose from the menu Data > Filter > Autofilter.  Filter on the "p-value" column to show only GO terms that have a p value of < 0.05.  '''''How many GO terms are associated with this profile at p < 0.05?'''''  The GO list also has a column called "Corrected p-value".  This correction is needed because the software has performed thousands of significance tests.  Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05.  '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
 ##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).

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 # '''Prepare your microarray data file for loading into STEM.'''
 #* Download your Excel workbook that you used for your [[Week 8]] assignment.
-#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
+#* Insert a new worksheet into your Excel workbook, and name it "dSWI4_stem".
-#* Select all of the data from your "(STRAIN)_ANOVA" worksheet and Paste special > paste values into your "(STRAIN)_stem" worksheet.
+#* Select all of the data from your "dSWI4_ANOVA" worksheet and Paste special > paste values into your "dSWI4_stem" worksheet.
 #** Your leftmost column should have the column header "Master_Index".  Rename this column to "SPOT".  Column B should be named "ID".  Rename this column to "Gene Symbol".  Delete the column named "Standard_Name".
 #** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
 #*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu.  Undo the filter.  This ensures that we will cluster only the genes with a "significant" change in expression and not the noise.  '''''Record the number of genes left in your electronic notebook.''''' - '''2643'''
-#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
+#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, dSWI4_AvgLogFC_t30, etc.).
 #** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
 #** Save your work.  Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt).  Click OK to the warnings and close your file.
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 ## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
 ##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
-##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table".  For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile.  In the window that appears, click on the "Save Table" button and save the file to your desktop.  Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
+##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table".  For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile.  In the window that appears, click on the "Save Table" button and save the file to your desktop.  Make your filename descriptive of the contents, e.g. "dSWI4_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
 ##** Upload these files to the wiki and link to them on your individual journal page.  (Note that it will be easier to zip all the files together and upload them as one file).
-##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile.  In the window that appears, click on the "Save Table" button and save the file to your desktop.  Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number.  At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
+##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile.  In the window that appears, click on the "Save Table" button and save the file to your desktop.  Make your filename descriptive of the contents, e.g. "dSWI4_profile#_GOlist.txt", where you replace the number symbol with the actual profile number.  At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
 ##** Upload these files to the wiki and link to them on your individual journal page.  (Note that it will be easier to zip all the files together and upload them as one file).
 # '''Analyzing and Interpreting STEM Results'''

← Older revision		Revision as of 23:03, 2 November 2017
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		+	=STEM results=
		+	[[Media:dSWI4_STEM_results_CW.zip\|dSWI4 STEM results]]
		+
	=Acknowledgments=		=Acknowledgments=