Icrespin Journal Week 8 - Revision history

Icrespin: /* Clustering and GO Term Enrichment with stem (part 2) */ fixed bullet list

2019-10-24T22:47:55Z

‎Clustering and GO Term Enrichment with stem (part 2): fixed bullet list

Icrespin: /* Clustering and GO Term Enrichment with stem (part 2) */ added info

2019-10-24T22:45:56Z

‎Clustering and GO Term Enrichment with stem (part 2): added info

Icrespin: /* Clustering and GO Term Enrichment with stem (part 2) */ added answer

2019-10-24T22:41:03Z

‎Clustering and GO Term Enrichment with stem (part 2): added answer

Icrespin: /* Clustering and GO Term Enrichment with stem (part 2) */ edited info

2019-10-24T22:36:40Z

‎Clustering and GO Term Enrichment with stem (part 2): edited info

Icrespin: /* Clustering and GO Term Enrichment with stem (part 2) */ answered questions

2019-10-24T22:31:09Z

‎Clustering and GO Term Enrichment with stem (part 2): answered questions

Icrespin: /* Data/Files */ added file

2019-10-24T22:25:11Z

‎Data/Files: added file

Icrespin: /* Data/Files */ edited name

2019-10-24T22:23:14Z

‎Data/Files: edited name

Icrespin: /* Data/Files */ edited file name

2019-10-24T22:22:43Z

‎Data/Files: edited file name

Icrespin: /* Data/Files */ added info

2019-10-24T22:22:01Z

‎Data/Files: added info

Icrespin: /* Clustering and GO Term Enrichment with stem (part 2) */ added more info

2019-10-24T22:14:42Z

‎Clustering and GO Term Enrichment with stem (part 2): added more info

@@ Line 177: / Line 177: @@
 ## 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?'''''
-###*Profile 1 (or in STEM it is profile 45) was selected because it was the first profile that comes up. It is interesting to see that it has an increase and then a sudden drop in its profile. It is cool to investigate because it isn't similar to the other profiles.
+##**Profile 1 (or in STEM it is profile 45) was selected because it was the first profile that comes up. It is interesting to see that it has an increase and then a sudden drop in its profile. It is cool to investigate because it isn't similar to the other profiles.
 ##* '''''How many genes belong to this profile?'''''
-##*406
+##**406
 ##* '''''How many genes were expected to belong to this profile?'''''
-##*29.9
+##**29.9
 ##* '''''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.
-##* 0.00
+##**0.00
 ##* 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?'''''
-##*69/157
+##**69/157
-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 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?'''''
-##*9/157
+##**9/157
 ##* 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 research presentation.  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.

@@ Line 184: / Line 184: @@
 ##* '''''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.
 ##* 0.00
-##* 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 research presentation.  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.

@@ Line 183: / Line 183: @@
 ##*29.9
 ##* '''''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).

@@ Line 179: / Line 179: @@
 ###*Profile 1 (or in STEM it is profile 45) was selected because it was the first profile that comes up. It is interesting to see that it has an increase and then a sudden drop in its profile. It is cool to investigate because it isn't similar to the other profiles.
 ##* '''''How many genes belong to this profile?'''''
-###*29.9
+##*406
 ##* '''''How many genes were expected to belong to this profile?'''''
-###*406
+##*29.9
 ##* '''''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?'''''

@@ Line 177: / Line 177: @@
 ## 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?'''''

← Older revision		Revision as of 22:25, 24 October 2019
Line 196:		Line 196:

	[[Media:Crespin2_BIOL367_F19_microarray-data_dGLN3.txt\| Text file of dGLN3 data]]		[[Media:Crespin2_BIOL367_F19_microarray-data_dGLN3.txt\| Text file of dGLN3 data]]
		+
		+	[[Media:Crespin_ALLstemprofiles.PNG\| Screenshot of all stem profiles]]

	[[Media:Crespin_dGLN3_profile_genelist.zip\| Zipped file of dGLN3 genelist]]		[[Media:Crespin_dGLN3_profile_genelist.zip\| Zipped file of dGLN3 genelist]]

@@ Line 199: / Line 199: @@
 [[Media:Crespin_dGLN3_profile_genelist.zip| Zipped file of dGLN3 genelist]]
-[[Media:Crespin_Signifcant profiles.zip| Zipped file of dGLN3 profile screenshots]]
+[[Media:Crespin_Significant_profiles.zip| Zipped file of dGLN3 profile screenshots]]
 == Conclusion ==

← Older revision		Revision as of 22:22, 24 October 2019
Line 196:		Line 196:

	[[Media:Crespin2_BIOL367_F19_microarray-data_dGLN3.txt\| Text file of dGLN3 data]]		[[Media:Crespin2_BIOL367_F19_microarray-data_dGLN3.txt\| Text file of dGLN3 data]]
		+
		+	[[Media:Crespin_dGLN3_profile_genelist.zip\| Zipped file of dGLN3 genelist]]
		+
		+	[[Media:Crespin_Signifcant_profiles.zip\| Zipped file of dGLN3 profile screenshots]]

	== Conclusion ==		== Conclusion ==

@@ Line 164: / Line 164: @@
 ## 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.
 == Data/Files ==