ArashLari Week 10 - Revision history

ArashLari: summary paragraph

2017-11-07T02:18:00Z

summary paragraph

ArashLari: /* Electronic Notebook */ added GO terms

2017-11-07T02:08:38Z

‎Electronic Notebook: added GO terms

ArashLari: /* Electronic Notebook */ updated answers

2017-11-07T01:45:07Z

‎Electronic Notebook: updated answers

ArashLari: /* Electronic Notebook */ answering more questions from part 5

2017-11-06T03:33:54Z

‎Electronic Notebook: answering more questions from part 5

ArashLari: /* Electronic Notebook */ Answering first questions about profile 2

2017-11-06T03:27:28Z

‎Electronic Notebook: Answering first questions about profile 2

ArashLari: /* File */ this is a link to all the files used for this assignment

2017-11-06T03:13:15Z

‎File: this is a link to all the files used for this assignment

ArashLari: /* File */ added my zip file

2017-11-06T03:12:05Z

‎File: added my zip file

ArashLari: /* Electronic Notebook */ added a special case for #DIV/0

2017-11-06T03:10:56Z

‎Electronic Notebook: added a special case for #DIV/0

ArashLari: /* Clustering and GO Term Enrichment with stem */ added our special case

2017-11-06T03:08:03Z

‎Clustering and GO Term Enrichment with stem: added our special case

ArashLari: /* Electronic Notebook */ replaced all instances of "(STRAIN)" with "dHMO1"

2017-11-06T03:06:41Z

‎Electronic Notebook: replaced all instances of "(STRAIN)" with "dHMO1"

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   Definition: A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
 '''''This is the stopping point for the Week 10 Assignment.''''' We will pick up the next steps in the analysis in subsequent weeks.
+== Summary of Knowledge ==
 ==Acknowledgements==
 Hayden and I worked on this assignment together, we compare results together in class and texted each other if we had any questions.

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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].
 '''''This is the stopping point for the Week 10 Assignment.''''' We will pick up the next steps in the analysis in subsequent weeks.

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   Answer the following:
 ##* '''''Why did you select this profile?  In other words, why was it interesting to you?'''''
-##* I chose this profile because it seemed to have an interesting reaction to cold shock. It showed a strong negative expression change at minute 30, but at minute 90 it seems that the genes seemed to have "bounced back" and expressed a similar (but less extreme) change in the positive range.
+##* I chose this profile because it seemed to have an interesting reaction to cold shock. It showed a strong negative expression change at minute 30, but at minute 90 it seems that the genes seemed to have "bounced back" and expressed a similar (but less extreme) change in the positive range. This is shown by the profile type of "(0, -2, -2, 0, 1  0)"
 ##* '''''How many genes belong to this profile?'''''
-##* There are 157 genes that belong to this profile.
+##* There are 49 genes assigned to this profile.
 ##* '''''How many genes were expected to belong to this profile?'''''
-##* There were around a 1000 genes that passed the p-value filter, so around that number of genes.
+##* There were 18.7 genes expected, so more genes than expected were effected.
 ##* '''''What is the p value for the enrichment of genes in this profile?'''''
-##* TODO
+##* The p value for the enrichment of genes in this profile is 2.1 E-9, so very small.
    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?'''''

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 ##* TODO
    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?'''''
+##* 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?'''''
 ##* 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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 ##** 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 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.'''''
 ##* '''''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.
+##* There were around a 1000 genes that passed the p-value filter, so around that number of genes.
 ##* 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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 ==File==
-[[File:Work.zip] This is a link to all the files used for this assignment]
+[[File:Work.zip]]
 ==Electronic Notebook==

← Older revision		Revision as of 03:12, 6 November 2017
Line 1:		Line 1:
	==File==		==File==
		+	[[File:Work.zip] This is a link to all the files used for this assignment]

	==Electronic Notebook==		==Electronic Notebook==

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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'''
 ## 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.

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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.'''''
 #** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).

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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 "dHMO1_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 "dHMO1_ANOVA" worksheet and Paste special > paste values into your "dHMO1_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).
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 '''''This is the stopping point for the Week 10 Assignment.''''' We will pick up the next steps in the analysis in subsequent weeks.
 ==Acknowledgements==
 Hayden and I worked on this assignment together, we compare results together in class and texted each other if we had any questions.