Simonwro120 Week 10 - Revision history

Simonwro120: added necessary files

2017-11-07T22:49:09Z

added necessary files

Simonwro120: finished week 10

2017-11-07T04:10:53Z

finished week 10

Simonwro120: Syntax

2017-11-07T00:48:00Z

Syntax

Simonwro120: added to notebook

2017-11-07T00:45:50Z

added to notebook

Simonwro120: more electronic notebook

2017-11-07T00:41:46Z

more electronic notebook

Simonwro120: syntax fix

2017-11-06T23:47:20Z

syntax fix

Simonwro120: added steps up to 5

2017-11-06T23:32:49Z

added steps up to 5

Simonwro120: got rid of background

2017-11-06T23:15:02Z

got rid of background

Simonwro120: deleted un used steps

2017-11-06T23:12:58Z

deleted un used steps

Simonwro120: syntax

2017-10-31T22:43:59Z

syntax

← Older revision		Revision as of 22:49, 7 November 2017
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	==Electronic Notebook with Instructions and Specifications==		==Electronic Notebook with Instructions and Specifications==
		+
		+	==Requested Files==
		+	[[media:SW_dCIN5_profile_List.zip\| dCIN5 Profiles for both GO terms and Gene Lists]]
		+

	===Clustering and GO Term Enrichment with STEM===		===Clustering and GO Term Enrichment with STEM===

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 ##**The p value for the enrichment of genes in this profile is 3.4E-98.
 ##* 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?'''''
-##**
+##**114 GO terms are associated with having a p value of < 0.05 for profile 22.
 ##* 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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 === References ===
- LMU BioDB 2017. (2017). Week 810 Retrieved October 31, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
+*LMU BioDB 2017. (2017). Week 10 Retrieved October 31, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 {{simonwro120}}

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 ===Clustering and GO Term Enrichment with STEM===
 #'''Prepare microarray data file for loading into STEM'''
 #*Download: [[Media:SW_Week8_xl.zip|Excel file for the ANOVA of dCIN5]]
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 ##**179 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).
 ##** 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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-==Home Work Instructions==
+==Electronic Notebook with Instructions and Specifications==
 ===Clustering and GO Term Enrichment with STEM===
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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?'''''

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 ==Home Work Instructions==
-=== Clustering and GO Term Enrichment with stem ===
+=Clustering and GO Term Enrichment with STEM=
-# '''Prepare your microarray data file for loading into STEM.'''
+#'''Prepare microarray data file for loading into STEM'''
-#* Download your Excel workbook that you used for your [[Week 8]] assignment.
+#*Download: [[Media:SW_Week8_xl.zip|Excel file for the ANOVA of dCIN5]]
-#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
+#* Insert a new worksheet into your Excel workbook, and name it "dCIN5_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 "dCIN5_ANOVA" worksheet and Paste special > paste values into your "dCIN5_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.'''''
 #** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, 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.
 #*** Note that you should turn on the file extensions if you have not already done so.
 # '''Now download and extract the STEM software.'''  [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
 #* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
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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.
+##**The first significant profile showed in detail, so we could screenshot it, but the six other significant profiles only should a blank white page when clicked on.
 ##** 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!
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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].
 === Acknowledgements ===
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 === References ===
 {{simonwro120}}

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 #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
 <b>Signature:</b> [[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 15:42, 31 October 2017 (PDT)
 === References ===