Bhamilton18 Week 10 - Revision history

Bhamilton18: Added conclusion

2017-11-06T22:02:36Z

Added conclusion

Bhamilton18: Added answers for Section #5 and definitions

2017-11-06T21:47:19Z

Added answers for Section #5 and definitions

Bhamilton18: added dHAP4 in the correct spots in the instructions

2017-11-06T21:17:59Z

added dHAP4 in the correct spots in the instructions

Bhamilton18: added p-value and list powerpoint with descriptions

2017-11-06T21:12:01Z

added p-value and list powerpoint with descriptions

Bhamilton18: Fixed excel link to correct excel document

2017-11-06T20:39:30Z

Fixed excel link to correct excel document

Bhamilton18: added excel files and screenshots

2017-11-02T23:12:39Z

added excel files and screenshots

Bhamilton18: Added File Uploads section

2017-11-02T22:55:55Z

Added File Uploads section

Bhamilton18: Deleted Extra steps

2017-11-02T22:53:27Z

Deleted Extra steps

Bhamilton18: Added steps from week 10 assignment

2017-11-02T22:00:22Z

Added steps from week 10 assignment

Show changes

Bhamilton18: Added Acknowledgments and References

2017-10-31T22:07:45Z

Added Acknowledgments and References

New page

==Acknowledgments==
#I worked with my partner [[User:Nicolekalcic| Nicole Kalcic]] this week. We messaged each other with questions as well as met in person.
#My excel work was based off of data given to me by Dr. Dahlquist and Dr. Dionisio.
#All instructions came from the [[Week 10]] instructions and were altered to fit my personal gene, dHAP4.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

==References==
LMU BioDB 2017. (2017). Week 10. Retrieved October 31, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10

{{Bhamilton18}}

[[Category: Journal Entry]]

@@ Line 47: / Line 47: @@
 ##** 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. '''''Profile #2'''''
 ##* '''''Why did you select this profile?  In other words, why was it interesting to you?'''''
-##* '''''How many genes belong to this profile?'''''
+##**This profile contained the most variation in it's data as well as appears to have the largest difference among the genes invovled.
-##* '''''How many genes were expected to belong to this profile?'''''
+##* '''''How many genes belong to this profile?''''' 63.0
-##* '''''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.
+##* '''''How many genes were expected to belong to this profile?''''' 41.0
-##* 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?'''''
+##* '''''What is the p value for the enrichment of genes in this profile?''''' 7.3 E-4
-##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 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 seventh column and then choose from the menu Data > Filter > Number Filters > Less Than 0.05. '''''How many GO terms are associated with this profile at p < 0.05?'''''  12
-##** 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.
+##**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?''''' 0
-##*** Note whether the same GO terms are showing up in multiple clusters.
+##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).  '''''I used plain p-value'''''
-##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org].  In your final presentation, you will discuss the biological interpretation of these GO terms.  In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?  Also, what does this have to do with the transcription factor being deleted (for the Δgln3 and Δswi4 groups)?'''''
+##** GO:2000112	regulation of cellular macromolecule biosynthetic process
-##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
+##** GO:0071496	cellular response to external stimulus
-##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
+##** GO:0009889	regulation of biosynthetic process
-##** 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"".
+##** GO:0009605	response to external stimulus
-##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
+##** GO:0032446	protein modification by small protein conjugation
 ==Acknowledgments==
@@ Line 66: / Line 77: @@
 #My excel work was based off of data given to me by Dr. Dahlquist and Dr. Dionisio.
 #All instructions came from the [[Week 10]] instructions and were altered to fit my personal gene, dHAP4.
 #'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

@@ Line 11: / Line 11: @@
 # '''Prepare your microarray data file for loading into STEM.'''
-#* Download your Excel workbook that you used for your [[Week 8]] assignment.
+#* Download Excel workbook from our [[Week 8]] assignment: [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017BVH1.zip | dHAP4 Excel Files]]
-#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
+#* Insert a new worksheet into your Excel workbook, and name it "dHAP4_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 "dHAP4_ANOVA" worksheet and Paste special > paste values into your "dHAP4_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.'''''
+#*** 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.  '''''There should be 1892 genes remaining.'''''
 #** 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.).

@@ Line 6: / Line 6: @@
 Stem Results Screenshots: [[Media:STEMProfiles(1)PPT_BVH.zip | STEM Profiles Powerpoint]]
-Zip Files of genelist/GOlist: [[Media: Profile_genelist_and_Golist.zip | Genelist and GOlist Profiles]]
+Zip Files of genelist/GOlist and p-values: [[Media: BIOL367_F17_sample_p-value_slide_BVH.zip | Genelist, GOlist and P-values Powerpoint]]
 === Clustering and GO Term Enrichment with stem ===

@@ Line 2: / Line 2: @@
 ===File Uploads===
-Excel Sheet: [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017BVH.zip | dHAP4 Excel Files]]
+Excel Sheet: [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017BVH1.zip | dHAP4 Excel Files]]
 Stem Results Screenshots: [[Media:STEMProfiles(1)PPT_BVH.zip | STEM Profiles Powerpoint]]

@@ Line 2: / Line 2: @@
 ===File Uploads===
-Excel Sheet:
+Excel Sheet: [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017BVH.zip | dHAP4 Excel Files]]
-Stem Results Screenshots:
+Stem Results Screenshots: [[Media:STEMProfiles(1)PPT_BVH.zip | STEM Profiles Powerpoint]]
-Zip Files of genelist:
+Zip Files of genelist/GOlist: [[Media: Profile_genelist_and_Golist.zip | Genelist and GOlist Profiles]]
 === Clustering and GO Term Enrichment with stem ===

@@ Line 73: / Line 73: @@
 ##* The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
 ==Acknowledgments==
 #I worked with my partner [[User:Nicolekalcic| Nicole Kalcic]] this week. We messaged each other with questions as well as met in person.

← Older revision		Revision as of 22:55, 2 November 2017
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	==Electronic Notebook Steps==		==Electronic Notebook Steps==
		+
		+	===File Uploads===
		+	Excel Sheet:
		+
		+	Stem Results Screenshots:
		+
		+	Zip Files of genelist:
		+
		+	Zip Files of GOlist:

	=== Clustering and GO Term Enrichment with stem ===		=== Clustering and GO Term Enrichment with stem ===