Hhinsch Week 10 - Revision history

Hhinsch: fixed a typo on my acknowledgments

2017-11-07T07:19:49Z

fixed a typo on my acknowledgments

Hhinsch: edited one of my answers for interpretation of STEM

2017-11-07T07:18:16Z

edited one of my answers for interpretation of STEM

Hhinsch: fixed the font on "here" to make it bold

2017-11-07T07:05:25Z

fixed the font on "here" to make it bold

Hhinsch: edited references

2017-11-07T07:04:40Z

edited references

Hhinsch: added links week 10 files and invoked template

2017-11-07T07:02:52Z

added links week 10 files and invoked template

Hhinsch: added my electronic signarute, electronic workbook summary and acknowledgments, and locations where the deliverable files can be downloaded

2017-11-07T06:40:46Z

added my electronic signarute, electronic workbook summary and acknowledgments, and locations where the deliverable files can be downloaded

Hhinsch: added acknowledgmnets and references and electronic workbook summary. saving just in case but not done

2017-11-07T06:27:31Z

added acknowledgmnets and references and electronic workbook summary. saving just in case but not done

Hhinsch: fixed the code for my gene cluster info

2017-11-07T06:11:50Z

fixed the code for my gene cluster info

Hhinsch: added some information to my gene clustering

2017-11-07T06:10:45Z

added some information to my gene clustering

Hhinsch: edited where my excel files can be accessed and substituted some of the assignment directions to fit my electronic workbook

2017-11-07T05:58:10Z

edited where my excel files can be accessed and substituted some of the assignment directions to fit my electronic workbook

@@ Line 85: / Line 85: @@
 #I worked with [[User:ArashLari]] over text and in class in order to compare results and make sure we did not use the same profile for the assignment.
 #Dr. Dahlquist helped by giving detailed steps in order to complete the deliverable for this assignment.
-#While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:40, 6 November 2017 (PST)
+#While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:40, 6 November 2017 (PST)
 ==References==

@@ Line 42: / Line 42: @@
 # '''Analyzing and Interpreting STEM Results'''
 ## Select the '''''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.'''''
-##* '''''I selected Profile 45 because it had a lot of genes assigned(158) and a few of the genes had a very large initial reaction to the cold shock.'''''
+##* '''''I selected Profile 45 because it had a lot of genes assigned(158) and a few of the genes had a very large reaction to the cold shock both initially and as time went on.'''''
 ##* '''''158 Genes belong to this profile.'''''
 ##* '''''19.1 Genes were expected to belong to this profile.'''''

@@ Line 76: / Line 76: @@
 ==Updated Excel File==
-*The updated excel file can be downloaded from ''Here:''' [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_-_HH.xlsx.zip|BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_-_HH.xlsx.zip]]
+*The updated excel file can be downloaded from '''Here:''' [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_-_HH.xlsx.zip|BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_-_HH.xlsx.zip]]
 ==Slides==

@@ Line 88: / Line 88: @@
 ==References==
+#LMU BioDB 2017. (2017). Week 10. Retrieved November 2, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 {{hhinsch}}

@@ Line 73: / Line 73: @@
 I learned that the genes in the dHMO1 strain did not have many significant results, seeing that we had to use the uncorrected p-value to analyze the data. The profile I used(#45) showed a varying change in expression, shutting off the genes then turning them back on as time went on. It seems the cold shock had a large effect on some of the genes, and others were not changed that much. Due to my lack of knowledge of molecular biology, I can only make an assumption, but I presume that the genes that were effected by the cold shock were turned off in order to preserve themselves, then turned back on as time went on and the temperature rose.
 ==Tab-Delimited Text Files created and used for STEM==
-*The tab-delimited text files created and used for STEM can be downloaded from '''Here:'''
+*The tab-delimited text files created and used for STEM can be downloaded from '''Here:'''[[Media:Tab_Delimited_Text_Files_HH.zip|Tab_Delimited_Text_Files_HH.zip]]
 ==Updated Excel File==
-*The updated excel file can be downloaded from ''Here:'''
+*The updated excel file can be downloaded from ''Here:''' [[Media:BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_-_HH.xlsx.zip|BIOL367_Fall2017_Dahlquist-microarray-data-master_20171017_-_HH.xlsx.zip]]
 ==Slides==
-*The slides that I created can be downloaded from '''Here:'''
+*The slides that I created can be downloaded from '''Here:''' [[Media:BIOL367_F17_dHMO1_slides_HH.zip|BIOL367_F17_dHMO1_slides_HH.zip]]
 ==Acknowledgments==
@@ Line 88: / Line 89: @@
 ==References==
-== Shared Journal Assignment ==
+{{hhinsch}}

@@ Line 69: / Line 69: @@
 *It seems that some of the genes really reduced their expression when the cold shock was induced, but went back to normal as time went by. At least that was the trend of most of the genes. However, a few of the genes changed drastically on the x-axis.
 *There were only a few genes left to choose from for the interpretation of the GO lists, but I decided to choose 6 from the corrected p-value on the Go list because this would have the most stringent constraints. I felt that these genes I chose would be more significant.
-*The slides that I created can be downloaded from '''Here''':
 ==Acknowledgments==
-#I worked with [[User:Arash Lari]]
+#I worked with [[User:ArashLari]] over text and in class in order to compare results and make sure we did not use the same profile for the assignment.
 == Shared Journal Assignment ==

@@ Line 61: / Line 61: @@
 ##***'''GO:0000470:maturation of LSU-rRNA''' <code>Ontology:biological_process</code> <code> Definition:Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule. Source: GOC:curators.</code>
 ##***'''GO:0000472:endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)''' <code>Ontology:biological_process</code> <code> Definition:Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA. Source: PMID:10690410, GOC:curators.</code>
-==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ====
+====This is the end of the Week 10 Assignment====
-In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time.  The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors.  We will explore this using the YEASTRACT database.
+== Electronic Workbook summary==
+*One should be able to follow the steps above in order to come to the same conclusions that I did.
-# Open the gene list in Excel for the one of the significant profiles from your stem analysis.  Choose a cluster with a clear cold shock/recovery up/down or down/up pattern.  You should also choose one of the largest clusters.
+*It should again be noted that because dHMO1 is a special case, we used the p-value in the first part of the assignment instead of the corrected p-value like other strains.
-#* Copy the list of gene IDs onto your clipboard.
+*This assignment was relatively straightforward. I chose Profile #45 because of the large amount of genes and the massive change in expression due to the cold shock.
-# Launch a web browser and go to the [http://www.yeastract.com/ YEASTRACT database].
+*It seems that some of the genes really reduced their expression when the cold shock was induced, but went back to normal as time went by. At least that was the trend of most of the genes. However, a few of the genes changed drastically on the x-axis.
-#* On the left panel of the window, click on the link to [http://www.yeastract.com/formrankbytf.php ''Rank by TF''].
+*There were only a few genes left to choose from for the interpretation of the GO lists, but I decided to choose 6 from the corrected p-value on the Go list because this would have the most stringent constraints. I felt that these genes I chose would be more significant.
-#* Paste your list of genes from your cluster into the box labeled ''ORFs/Genes''.
+*The slides that I created can be downloaded from '''Here''':
-#* Check the box for ''Check for all TFs''.
+==Acknowledgments==
-#* Accept the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
+#I worked with [[User:Arash Lari]]
 == Shared Journal Assignment ==

@@ Line 57: / Line 57: @@
 ##***'''GO:0090502:RNA phosphodiester bond hydrolysis, endonucleolytic''' <code>Ontology:biological_process</code> <code>Definition:The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. Source: GOC:dph, GOC:tb.</code>
 ##***'''GO:0000966:RNA 5'-end processing'''<code>Ontology:biological_process</code> <code>Definition:Any process involved in forming the mature 5' end of an RNA molecule. Source: GOC:krc.</code>
-##***'''GO:0044238:primary metabolic process''' <code>Ontology:biological_process</code> <code> Definition:The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. Source: GOC:go_curators, [http://www.metacyc.org http://www.metacyc.org].<code>
+##***'''GO:0044238:primary metabolic process''' <code>Ontology:biological_process</code> <code> Definition:The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. Source: GOC:go_curators, [http://www.metacyc.org http://www.metacyc.org].</code>
 ##***'''GO:0006807:nitrogen compound metabolic process''' <code>Ontology:biological_process</code> <code>Definition:The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. Source: GOC:go_curators, CHEBI:51143, GOC:jl, ISBN:0198506732.</code>
 ##***'''GO:0000470:maturation of LSU-rRNA''' <code>Ontology:biological_process</code> <code> Definition:Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule. Source: GOC:curators.</code>

@@ Line 55: / Line 55: @@
 ##** 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].
-##***'''GO:0090502:RNA phosphodiester bond hydrolysis, endonucleolytic''' :The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. Source: GOC:dph, GOC:tb.
+##***'''GO:0090502:RNA phosphodiester bond hydrolysis, endonucleolytic''' <code>Ontology:biological_process</code> <code>Definition:The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. Source: GOC:dph, GOC:tb.</code>
-##***'''GO:0000966:RNA 5'-end processing''' :Any process involved in forming the mature 5' end of an RNA molecule. Source: GOC:krc.
+##***'''GO:0000966:RNA 5'-end processing'''<code>Ontology:biological_process</code> <code>Definition:Any process involved in forming the mature 5' end of an RNA molecule. Source: GOC:krc.</code>
-##***'''GO:0044238:primary metabolic process''' :The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. Source: GOC:go_curators, [http://www.metacyc.org http://www.metacyc.org].
+##***'''GO:0044238:primary metabolic process''' <code>Ontology:biological_process</code> <code> Definition:The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. Source: GOC:go_curators, [http://www.metacyc.org http://www.metacyc.org].<code>
-##***'''GO:0006807:nitrogen compound metabolic process''' :The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. Source: GOC:go_curators, CHEBI:51143, GOC:jl, ISBN:0198506732.
+##***'''GO:0006807:nitrogen compound metabolic process''' <code>Ontology:biological_process</code> <code>Definition:The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. Source: GOC:go_curators, CHEBI:51143, GOC:jl, ISBN:0198506732.</code>
-##***'''GO:0000470:maturation of LSU-rRNA''' :Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule. Source: GOC:curators.
+##***'''GO:0000470:maturation of LSU-rRNA''' <code>Ontology:biological_process</code> <code> Definition:Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule. Source: GOC:curators.</code>
-##***'''GO:0000472:endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)''' :Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA. Source: PMID:10690410, GOC:curators.
+##***'''GO:0000472:endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)''' <code>Ontology:biological_process</code> <code> Definition:Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA. Source: PMID:10690410, GOC:curators.</code>
 ==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ====

@@ Line 1: / Line 1: @@
 == Clustering and GO Term Enrichment with stem ==
-====.zip file====
 # '''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 "dHMO1_stem".
-#* Select all of the data from your "(STRAIN)_ANOVA" worksheet and Paste special > paste values into your "dHMO1_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 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.  '''There are 1055 genes left.'''
-#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
+#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, dHMO1_AvgLogFC_t15, etc.).
 #** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
 #** 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.
@@ Line 35: / Line 36: @@
 ## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
 ##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
-##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table".  For each of the profiles, click on the "Profile Gene Table" button to see the list of genes 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#_genelist.txt", where you replace the number symbol with the actual profile number.
+##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table".  For each of the profiles, click on the "Profile Gene Table" button to see the list of genes 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. "dHMO1_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
 ##** [[Media:dHMO1_genelists.zip|dHMO1_genelists.zip]]
-##* 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!
+##* 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. "dHMO1_profile#_GOlist.txt", where you use "dHMO1", 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!
 ##**[[Media:dHMO1_GOlists.zip|dHMO1_GOlists.zip]]
 # '''Analyzing and Interpreting STEM Results'''
-## Select the '''''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:
+## Select the '''''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.'''''
 ##* '''''I selected Profile 45 because it had a lot of genes assigned(158) and a few of the genes had a very large initial reaction to the cold shock.'''''
 ##* '''''158 Genes belong to this profile.'''''