Kwrigh35 Week 10 - Revision history

Kwrigh35: /* Deliverables */ formatting change

2017-11-03T00:12:18Z

‎Deliverables: formatting change

Kwrigh35: /* Deliverables */ added links to deliverables

2017-11-03T00:11:48Z

‎Deliverables: added links to deliverables

Kwrigh35: /* Acknowledgements */ added acknowledgements

2017-11-02T23:54:45Z

‎Acknowledgements: added acknowledgements

Kwrigh35: /* Analyzing and Interpreting STEM Results */ added answers

2017-11-02T23:49:10Z

‎Analyzing and Interpreting STEM Results: added answers

Kwrigh35: /* Electronic Notebook: Clustering and GO Term Enrichment with stem */ added deliverables section

2017-11-02T23:19:47Z

‎Electronic Notebook: Clustering and GO Term Enrichment with stem: added deliverables section

Kwrigh35: /* Electronic Notebook: Clustering and GO Term Enrichment with stem */ fixed list levels

2017-11-02T23:18:48Z

‎Electronic Notebook: Clustering and GO Term Enrichment with stem: fixed list levels

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Kwrigh35: /* Prepare your microarray data file for loading into STEM */ fixed syntax

2017-11-02T23:15:39Z

‎Prepare your microarray data file for loading into STEM: fixed syntax

Kwrigh35: /* Prepare your microarray data file for loading into STEM */ changed answer text to red

2017-11-02T23:13:51Z

‎Prepare your microarray data file for loading into STEM: changed answer text to red

Kwrigh35: /* Prepare your microarray data file for loading into STEM */ highlighted answer

2017-11-02T23:12:35Z

‎Prepare your microarray data file for loading into STEM: highlighted answer

Kwrigh35: /* Electronic Notebook: Clustering and GO Term Enrichment with stem */ made steps into separate sectoins

2017-11-02T23:07:02Z

‎Electronic Notebook: Clustering and GO Term Enrichment with stem: made steps into separate sectoins

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 ==Deliverables==
 [[media:DZAP1_STEM_Results_Kwrigh35.zip | STEM Results]] including tab-delimited files and ppt with results.
 [[media:dZAP1_ANOVA_KWRIGH35.zip | Updated Excel Workbook]] including STEM page.

← Older revision		Revision as of 00:11, 3 November 2017
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	==Deliverables==		==Deliverables==
		+	[[media:DZAP1_STEM_Results_Kwrigh35.zip \| STEM Results]] including tab-delimited files and ppt with results.
		+	[[media:dZAP1_ANOVA_KWRIGH35.zip \| Updated Excel Workbook]] including STEM page.

	==Electronic Notebook: Clustering and GO Term Enrichment with stem==		==Electronic Notebook: Clustering and GO Term Enrichment with stem==

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 ==Acknowledgements==
 ==References==
 LMU BioDB 2017. (2017). Week 10. Retrieved October 17, 2017, from [[Week 10]]

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 *** 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===
-* 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:
+* Select '''''one''''' of the profiles you saved in the previous step for further interpretation 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?'''''
+*** The p-value is 0.  The p-value is most likely not actually 0, but rounded to 0 since the number was so small.
 ** 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.

← Older revision		Revision as of 23:19, 2 November 2017
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		+	==Deliverables==
		+
	==Electronic Notebook: Clustering and GO Term Enrichment with stem==		==Electronic Notebook: Clustering and GO Term Enrichment with stem==
	===Prepare your microarray data file for loading into STEM===		===Prepare your microarray data file for loading into STEM===

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 #** 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].
+===Now download and extract the STEM software===
 #* 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.
 #* Unzip the file.  In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.

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 #** 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.''''' {{font color||yellow|1785 genes left}}
+#*** 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.''''' <span style="color:red">1785 genes left</span>
 #** 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.).

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 ==Electronic Notebook: Clustering and GO Term Enrichment with stem==
+===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".
@@ Line 12: / Line 11: @@
 #** 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].
+===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.
 #* Unzip the file.  In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
@@ Line 20: / Line 19: @@
 #*** You will need to navigate to the directory (folder) in which the STEM program resides.  If you followed the instructions above and extracted the stem folder to the Desktop, type the following:  <code>cd Desktop\stem</code>  and press "Enter".
 #*** To launch the program then type:  <code>java -mx512M -jar stem.jar -d defaults.txt</code>  and press "Enter".  This will launch the program with less memory allocated to it.-->
-# '''Running STEM'''
+===Running STEM===
 ## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
 ##* Click on the radio button ''No normalization/add 0''.
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 ## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
 ## In section 4 (Execute) click on the yellow Execute button to run STEM.
-# '''Viewing and Saving STEM Results'''
+===Viewing and Saving STEM Results===
 ## A new window will open called "All STEM Profiles (1)".  Each box corresponds to a model expression profile.  Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value.  Profiles with the same color belong to the same cluster of profiles.  The number in each box is simply an ID number for the profile.
 ##* Click on the button that says "Interface Options...".  At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time".  Then close the Interface Options window.
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 ##* 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!
 ##** 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'''
+===Analyzing and Interpreting STEM Results===
 ## 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?'''''