Difference between revisions of "Week 7"
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| − | + | '''This journal entry is due on Thursday, October 10, at midnight PDT.''' ''(Wednesday night/Thursday morning)'' '''''Note different due date (so that you don't have something due on the eve of "Autumn Day".''''' | |
| − | + | {{Individual Journal Instructions|week=7}} | |
| − | + | === Introduction to Microarrays === | |
| − | + | '''''Note: we are not assigning partners for this week. You are free to consult your classmates on the homework, but your answers on your individual journal entries must be in your own words.''''' | |
| − | + | ==== Read ==== | |
| + | |||
| + | * Campbell, A.M. and Heyer, L.J. (2003), "Chapter 4: Basic Research with DNA Microarrays", in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D (Available on MyLMUConnect; the color figures are also posted there)] | ||
| + | * [http://www.sciencemag.org/content/278/5338/680.full?sid=542f6cc5-016c-4cea-83af-1ea62867993e DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 278: 680-686.] | ||
| + | * [http://www.bio.davidson.edu/courses/genomics/chip/chip.html This animation from Malcolm Campbell may also be helpful.] | ||
| + | |||
| + | ==== Answer the following Discovery Questions from Chapter 4==== | ||
| + | |||
| + | '''5.''' (p. 110) Choose two genes from Figure 4.6 [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D (PDF of figures on MyLMUConnect)] and draw a graph to represent the change in transcription over time. | ||
| + | '''<nowiki>*</nowiki> | ||
| + | |||
| + | : ''Note: You can do this by hand and submit a hard copy in class on Thursday, October 10 (morning after the midnight deadline) or you may do it by computer and upload it to your individual journal page by the midnight deadline.'' | ||
| + | |||
| + | '''6b.''' (p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b. | ||
| + | |||
| + | '''7.''' (p. 110) Were any of the genes in Figure 4.7b transcribed similarly? | ||
| + | |||
| + | '''9.''' (p. 118) Why would most spots be yellow at the first time point? | ||
| + | |||
| + | '''10.''' (p. 118) Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food). | ||
| + | |||
| + | '''11.''' (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out? | ||
| + | |||
| + | '''12.''' (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously? | ||
| + | |||
| + | '''13.''' (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted? | ||
| + | |||
| + | '''14.''' (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed? | ||
| + | |||
| + | '''15.''' (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene? | ||
| + | |||
| + | '''16.''' (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene? | ||
| + | |||
| + | |||
| + | {{Shared Journal Instructions|week=7}} | ||
| + | |||
| + | ==== View ==== | ||
| + | |||
| + | * Watch the video [http://www.cbsnews.com/video/watch/?id=7398476n "Deception at Duke" from CBS ''60 Minutes'']. | ||
| + | |||
| + | ==== Reflection ==== | ||
| + | |||
| + | * Answer the following questions: | ||
| + | ** Were you aware of this case of research fraud before viewing this video? | ||
| + | ** What are your initial reactions to hearing about this case? | ||
| + | ** What role did data sharing play in uncovering this fraud? | ||
| + | ** What additional information would you like to know about this case? (We will be visiting it again in subsequent weeks in the course.) | ||
| + | * Please feel free to respond or comment on your classmates' reflections. | ||
| + | |||
| + | <!-- Old Assignment | ||
| + | == Overview of Microarray Data Analysis == | ||
This is a list of steps required to analyze DNA microarray data. | This is a list of steps required to analyze DNA microarray data. | ||
| Line 32: | Line 82: | ||
# Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this) | # Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this) | ||
# Map onto biological pathways (we will use GenMAPP for this) | # Map onto biological pathways (we will use GenMAPP for this) | ||
| − | + | ||
| + | ==== Analysis of ''Vibrio cholerae'' Microarray Data ==== | ||
* For the next section of the course, you will be introduced to the process we will use for the final projects in the course in a series of in-class and journal assignments where we will first analyze microarray data from ''Vibrio cholerae'', and then learn how to create a Gene Database for this organism. | * For the next section of the course, you will be introduced to the process we will use for the final projects in the course in a series of in-class and journal assignments where we will first analyze microarray data from ''Vibrio cholerae'', and then learn how to create a Gene Database for this organism. | ||
* The detailed instructions for the microarray data analysis we will carry out can be found on the [[BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae | Sample Microarray Analysis for ''Vibrio cholerae'' page]]. | * The detailed instructions for the microarray data analysis we will carry out can be found on the [[BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae | Sample Microarray Analysis for ''Vibrio cholerae'' page]]. | ||
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=== Background Readings === | === Background Readings === | ||
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//[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) link to full text] | //[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) link to full text] | ||
#Paper4 pmid=12050664 | #Paper4 pmid=12050664 | ||
| − | //[http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) link to full text], [[Media:Merrell_Compiled_Raw_Data_Vibrio.xls | dataset]] (on this wiki)<!--start at between-chip normalization | + | //[http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) link to full text], [[Media:Merrell_Compiled_Raw_Data_Vibrio.xls | dataset]] (on this wiki)<!--start at between-chip normalization |
</biblio> | </biblio> | ||
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* To be determined | * To be determined | ||
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Latest revision as of 19:29, 24 September 2013
This journal entry is due on Thursday, October 10, at midnight PDT. (Wednesday night/Thursday morning) Note different due date (so that you don't have something due on the eve of "Autumn Day".
Contents |
[edit] Individual Journal Assignment
- Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).
- Link from your user page to this Assignment page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
- Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
[edit] Introduction to Microarrays
Note: we are not assigning partners for this week. You are free to consult your classmates on the homework, but your answers on your individual journal entries must be in your own words.
[edit] Read
- Campbell, A.M. and Heyer, L.J. (2003), "Chapter 4: Basic Research with DNA Microarrays", in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. (Available on MyLMUConnect; the color figures are also posted there)
- DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 278: 680-686.
- This animation from Malcolm Campbell may also be helpful.
[edit] Answer the following Discovery Questions from Chapter 4
5. (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time. *
- Note: You can do this by hand and submit a hard copy in class on Thursday, October 10 (morning after the midnight deadline) or you may do it by computer and upload it to your individual journal page by the midnight deadline.
6b. (p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
9. (p. 118) Why would most spots be yellow at the first time point?
10. (p. 118) Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
13. (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
16. (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?
[edit]
- Store your journal entry in the shared Class Journal Week 7 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
- Link to your journal entry from your user page.
- Link back from the journal entry to your user page.
- NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
[edit] View
- Watch the video "Deception at Duke" from CBS 60 Minutes.
[edit] Reflection
- Answer the following questions:
- Were you aware of this case of research fraud before viewing this video?
- What are your initial reactions to hearing about this case?
- What role did data sharing play in uncovering this fraud?
- What additional information would you like to know about this case? (We will be visiting it again in subsequent weeks in the course.)
- Please feel free to respond or comment on your classmates' reflections.
