Cazinge Week 10 - Revision history

Cazinge: Added acknowledgements and references and template

2017-11-06T23:43:37Z

Added acknowledgements and references and template

Cazinge: /* Summary of what you need to turn in for the individual Week 10 assignment */

2017-11-06T23:40:57Z

‎Summary of what you need to turn in for the individual Week 10 assignment

Cazinge: updating to my gene

2017-11-06T23:25:15Z

updating to my gene

Cazinge: /* Clustering and GO Term Enrichment with stem */ formatting

2017-11-06T23:09:11Z

‎Clustering and GO Term Enrichment with stem: formatting

Cazinge: /* Clustering and GO Term Enrichment with stem */ adding reasons for cold shock

2017-11-06T23:08:01Z

‎Clustering and GO Term Enrichment with stem: adding reasons for cold shock

Cazinge: /* Clustering and GO Term Enrichment with stem */ filling out template

2017-11-06T22:45:43Z

‎Clustering and GO Term Enrichment with stem: filling out template

Cazinge: /* Clustering and GO Term Enrichment with stem */ templating responses

2017-11-06T22:43:06Z

‎Clustering and GO Term Enrichment with stem: templating responses

Cazinge: /* Clustering and GO Term Enrichment with stem */ adding answers

2017-11-06T22:39:53Z

‎Clustering and GO Term Enrichment with stem: adding answers

Cazinge: Adding answers

2017-11-06T22:28:17Z

Adding answers

Cazinge: /* Clustering and GO Term Enrichment with stem */ added notice

2017-11-06T22:12:57Z

‎Clustering and GO Term Enrichment with stem: added notice

← Older revision		Revision as of 23:43, 6 November 2017
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	In this experiment, we (almost) finished analyzing the DNA microarray dataset from Dahlquist's wetlab via a STEM analysis of the data. After pruning our data set solely to the p values and AvgLogFC's per timepoint for each gene, we ran our data through the STEM software provided to us. This produced a number of profiles comprised of genes expression curves and associated genes which had similar shapes to one another. After formatting and uploading this data to the wiki, I filtered the data in profile 22, taking only those that had corrected p values only .05, and found explanations as to why the genes in 6 of the profile's categories became expressed during cold shock. Due to time constraints, this is where the Week 10 assignment ends.		In this experiment, we (almost) finished analyzing the DNA microarray dataset from Dahlquist's wetlab via a STEM analysis of the data. After pruning our data set solely to the p values and AvgLogFC's per timepoint for each gene, we ran our data through the STEM software provided to us. This produced a number of profiles comprised of genes expression curves and associated genes which had similar shapes to one another. After formatting and uploading this data to the wiki, I filtered the data in profile 22, taking only those that had corrected p values only .05, and found explanations as to why the genes in 6 of the profile's categories became expressed during cold shock. Due to time constraints, this is where the Week 10 assignment ends.
		+
		+
		+	==Acknowledgements==
		+
		+	#Met outside of class with [[User:Emmatyrnauer\|Emma Tyrnauer]] to discuss any questions we had prior to meeting and throughout the process of completing the Week 10 assignment.
		+
		+	'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
		+
		+	[[User:Cazinge\|Cazinge]] ([[User talk:Cazinge\|talk]]) 15:43, 6 November 2017 (PST)
		+	==References==
		+
		+	#LMU BioDB 2017. (2017). Week 10. Retrieved November 3, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
		+	#Gene Ontology Consortium. (2017). Retrieved November 3, 2017, from http://geneontology.org
		+
		+	{{Template:Cazinge}}

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 #* Select the menu item File > Open and select the regulation matrix .xlsx file that has the "network" worksheet in it that you formatted above.  If the file has been formatted properly, GRNsight should automatically create a graph of your network.  Move the nodes (genes) around until you get a layout that you like and take a screenshot of the results.  Paste it into your PowerPoint presentation.
-==== Summary of what you need to turn in for the individual Week 10 assignment ====
+==== Conclusion ====
-# Your individual journal page should have an '''''electronic lab notebook''''' recording your work.  This includes the detailed methods specific to your analysis, your result files, the answers to any questions posed in the protocol above, a scientific conclusion, and the acknowledgments and references sections.  Don't forget your paragraph which is a biological interpretation of your stem results.
+In this experiment, we (almost) finished analyzing the DNA microarray dataset from Dahlquist's wetlab via a STEM analysis of the data. After pruning our data set solely to the p values and AvgLogFC's per timepoint for each gene, we ran our data through the STEM software provided to us. This produced a number of profiles comprised of genes expression curves and associated genes which had similar shapes to one another. After formatting and uploading this data to the wiki, I filtered the data in profile 22, taking only those that had corrected p values only .05, and found explanations as to why the genes in 6 of the profile's categories became expressed during cold shock. Due to time constraints, this is where the Week 10 assignment ends.

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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 "wt_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 "wt_ANOVA" worksheet and Paste special > paste values into your "wt_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).

@@ Line 77: / Line 77: @@
 ##**'''''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)?'''''
 ##*** '''ANSWER:'''
-##**** cytoplasm: Genes associated with cytoplasm are expressed when cold shock occurs as the cell undergoes a period of stress, due to the cytoplasm's need for more energy.
+##**** '''cytoplasm:''' Genes associated with cytoplasm are expressed when cold shock occurs as the cell undergoes a period of stress, due to the cytoplasm's need for more energy.
-##**** carbohydrate derivative metabolic process: During cold shock, the cell attempts to produce carbohydrates for oxidation, thus expressing genes of this category.
+##**** '''carbohydrate derivative metabolic process:''' During cold shock, the cell attempts to produce carbohydrates for oxidation, thus expressing genes of this category.
-##**** nucleotide metabolic process: When the cell experiences a period of stress due to cold shock, it attempts to generate energy via nucleotide metabolic processes, causing it to express genes associated with this category.
+##**** '''nucleotide metabolic process:''' When the cell experiences a period of stress due to cold shock, it attempts to generate energy via nucleotide metabolic processes, causing it to express genes associated with this category.
-##**** perioxidase activity: During cold shock, the cell attempts oxidation, causing genes associated with perioxidase activity to become expressed.
+##**** '''perioxidase activity:''' During cold shock, the cell attempts oxidation, causing genes associated with perioxidase activity to become expressed.
-##**** cellular response to toxic substance: A cell in cold shock exhibits similar characteristics as cells responding to toxic substances, causing genes of the latter category to be expressed.
+##**** '''cellular response to toxic substance:''' A cell in cold shock exhibits similar characteristics as cells responding to toxic substances, causing genes of the latter category to be expressed.
-##**** organophosphate metabolic process: During cold shock, the cell attempts to produce phosphate for oxidation, thus expressing genes of this category.
+##**** '''organophosphate metabolic process:''' During cold shock, the cell attempts to produce phosphate for oxidation, thus expressing genes of this category.
 ##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
 ##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".

@@ Line 77: / Line 77: @@
 ##**'''''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)?'''''
 ##*** '''ANSWER:'''
-##**** cytoplasm:
+##**** cytoplasm: Genes associated with cytoplasm are expressed when cold shock occurs as the cell undergoes a period of stress, due to the cytoplasm's need for more energy.
-##**** nucleotide metabolic process:
+##**** carbohydrate derivative metabolic process: During cold shock, the cell attempts to produce carbohydrates for oxidation, thus expressing genes of this category.
-##**** perioxidase activity:
+##**** nucleotide metabolic process: When the cell experiences a period of stress due to cold shock, it attempts to generate energy via nucleotide metabolic processes, causing it to express genes associated with this category.
-##**** cellular response to toxic substance:
+##**** perioxidase activity: During cold shock, the cell attempts oxidation, causing genes associated with perioxidase activity to become expressed.
-##**** organophosphate metabolic process:
+##**** cellular response to toxic substance: A cell in cold shock exhibits similar characteristics as cells responding to toxic substances, causing genes of the latter category to be expressed.
-##**** carbohydrate-derivative metabolic process:
+##**** organophosphate metabolic process: During cold shock, the cell attempts to produce phosphate for oxidation, thus expressing genes of this category.
 ##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
 ##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".

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 ##** '''ANSWER:''' 5.9E-181 (significant)
 ##* 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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 ## 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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 ##** 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].
 ==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ====