Week 10 - Revision history

Kdahlquist: /* Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes */ raised level of header

2017-11-21T00:50:42Z

‎Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: raised level of header

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

2017-11-02T22:58:30Z

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

Kdahlquist: /* Clustering and GO Term Enrichment with stem */ removed extraneous question

2017-11-02T22:57:27Z

‎Clustering and GO Term Enrichment with stem: removed extraneous question

Kdahlquist: /* Clustering and GO Term Enrichment with stem */ noted new stopping point

2017-11-02T22:54:24Z

‎Clustering and GO Term Enrichment with stem: noted new stopping point

Kdahlquist: remove under construction flag

2017-11-02T21:23:49Z

remove under construction flag

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

2017-11-02T21:23:08Z

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

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

2017-11-02T21:22:28Z

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

Kdahlquist: /* Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes */ clarify your transcription factor

2017-11-02T21:18:10Z

‎Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes: clarify your transcription factor

Kdahlquist: /* Objectives */ added purpose

2017-11-02T21:15:24Z

‎Objectives: added purpose

Kdahlquist: /* Reflect */ changed 10 to 8

2017-10-26T22:26:52Z

‎Reflect: changed 10 to 8

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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.
-==== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ====
+=== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ===
 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.

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 # 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.
 # Upload your updated Excel spreadsheet to the wiki that has today's manipulations in it.  Use the same filename as before so that the download link that you already (previous versions will still be available in the history).
-# Append the screenshots of the stem results to the PowerPoint presentation that contains the p value table that you created for the [[Week 8]] assignments.  Each slide in the presentation should have a meaningful title that describes the main message of the slide. Include the screenshot of the GRNsight-visualized network in the PowerPoint.
+# Append the screenshots of the stem results to the PowerPoint presentation that contains the p value table that you created for the [[Week 8]] assignments.  Each slide in the presentation should have a meaningful title that describes the main message of the slide.
 # Zip together all of the tab-delimited text files that you created for and from stem and upload them to the wiki.
 #* the file that was saved from your original spreadsheet that you used to run stem

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 ##* 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.
-##*** Note whether the same GO terms are showing up in multiple clusters.
+##**'''''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 that was deleted from your strain?'''''
 ##** 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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 ##** 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 ====

← Older revision		Revision as of 21:23, 2 November 2017
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−	~~{{Under_Construction}}~~
−
	'''This journal entry is due on Tuesday, November 7, at 12:01 AM PDT.'''		'''This journal entry is due on Tuesday, November 7, at 12:01 AM PDT.'''

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 #* the file that was saved from your original spreadsheet that you used to run stem
 #* each of the genelist and GOlist files for each of your significant profiles.
-# The shared journal assignment below.
+# Write a paragraph-length conclusion for this week's exercise.
 == Shared Journal Assignment ==

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 #* '''''Copy the table of results from the web page and paste it into a new Excel workbook to preserve the results.'''''
 #** '''''Upload the Excel file to OWW or Box and link to it in your electronic lab notebook.'''''
-#** '''''Are GLN3 or HAP4 on the list?  If so, what is their "% in user set", "% in YEASTRACT", and "p value".'''''
+#** '''''Is your transcription factor on the list?  If so, what is their "% in user set", "% in YEASTRACT", and "p value".''''' (Note that this doesn't apply to the wt strain).
-# For the mathematical model that we will build, we need to define a ''gene regulatory network'' of transcription factors that regulate other transcription factors.  We can use YEASTRACT to assist us with creating the network.  We want to generate a network with approximately 15-30 transcription factors in it.
+# For the mathematical model and GRNsight, we need to define a ''gene regulatory network'' of transcription factors that regulate other transcription factors.  We can use YEASTRACT to assist us with creating the network.  We want to generate a network with approximately 15-30 transcription factors in it.
 #* You need to select from this list of "significant" transcription factors, which ones you will use to run the model.  You will use these transcription factors and add GLN3 and HAP4 if they are not in your list.  Explain in your electronic notebook how you decided on which transcription factors to include.  Record the list and your justification in your electronic lab notebook.
 #* Go back to the YEASTRACT database and follow the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''.
-#* Copy and paste the list of transcription factors you identified (plus HAP4 and GLN3) into both the "Transcription factors" field and the "Target ORF/Genes" field.
+#* Copy and paste the list of transcription factors you identified (plus the transcription factor deleted in your strain) into both the "Transcription factors" field and the "Target ORF/Genes" field.
 #* We are going to use the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"
 #** Click the "Generate" button.

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 The purpose of this assignment is:
+* to perform "high level" analysis on microarray data in preparation for the final research project.
 == Individual Journal Assignment ==

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 === Reflect ===
-This week marks the end of Part 2 "Going Deeper" unit of the course.  At this point in the semester, you have worked with 10 other people in the class as partners on journal assignments.  Next week, you will be placed on teams of four that you will stay with throughout the rest of the semester.  Ultimately the teams will be assigned by Drs. Dahlquist and Dionsio based on balancing areas of expertise amongst the team members. However, we will also be gathering your input into the formation of the teams. In class on Thursday, November 2, you will confidentially fill out a card giving us the names of three other people in the class whom you want to be on your team (you can also choose people that haven't been your journal partner yet) and one person whom you prefer not to be on your team.
+This week marks the end of Part 2 "Going Deeper" unit of the course.  At this point in the semester, you have worked with 8 other people in the class as partners on journal assignments.  Next week, you will be placed on teams of four that you will stay with throughout the rest of the semester.  Ultimately the teams will be assigned by Drs. Dahlquist and Dionsio based on balancing areas of expertise amongst the team members. However, we will also be gathering your input into the formation of the teams. In class on Thursday, November 2, you will confidentially fill out a card giving us the names of three other people in the class whom you want to be on your team (you can also choose people that haven't been your journal partner yet) and one person whom you prefer not to be on your team.
 As we get ready for the team projects, we are asking you to reflect upon working in teams either in this class or in previous classes.