Dmadere Week 6 - Revision history

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	*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.		*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.
	*Wiki page creation details and assignment updates as listed by LMU BioDB 2019. (2019). Week 1. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1		*Wiki page creation details and assignment updates as listed by LMU BioDB 2019. (2019). Week 1. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
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 *I consulted my homework partner [[User:Mavila9|Marcus]] with any questions that I may have had.
 *I consulted the Wiki Help page when designing my home page as well. [[http://mediawiki.org/wiki/Help:Contents Help Page]]
-*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
+*'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''
 *[[User:Dmadere|Dmadere]] ([[User talk:Dmadere|talk]]) 23:32, 9 October 2019 (PDT)

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	=='''References'''==		=='''References'''==
		+	*Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays
		+	*Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
		+	*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.
		+	*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.
		+	*Wiki page creation details and assignment updates as listed by LMU BioDB 2019. (2019). Week 1. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1

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	=='''Acknowledgements'''==		=='''Acknowledgements'''==
		+	*I consulted my homework partner [[User:Mavila9\|Marcus]] with any questions that I may have had.
		+	*I consulted the Wiki Help page when designing my home page as well. [[http://mediawiki.org/wiki/Help:Contents Help Page]]
		+	*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
		+	*[[User:Dmadere\|Dmadere]] ([[User talk:Dmadere\|talk]]) 23:32, 9 October 2019 (PDT)

	=='''References'''==		=='''References'''==

← Older revision		Revision as of 06:27, 10 October 2019
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	=='''Purpose'''==		=='''Purpose'''==
		+	The purpose of this assignment was to understand DNA Microarrays and learn how to interpret its results based on the color of the results and the quantitative changes in transcription.

	=='''Questions'''==		=='''Questions'''==

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 *(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
-**The TCA cycle genes are induced due to the lack of glucose because they are able to
+**The TCA cycle genes are induced due to the lack of glucose because they are able to convert alcohol products, so they do not need glucose to function.
-#(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
+*(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
-#(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?
+**The guilt by association method can be used to ensure genes for enzymes in a common pathway are induced or repressed at the same time. This will allow for a prediction of the gene expression, and a microarray can be done to confirm.
-#(Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?
-#(Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?
+*(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?
 =='''Acknowledgements'''==
 =='''References'''==

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 **Gene X and Gene Y were transcribed similarly. Based on the colors representing the protein folds, the colors came out to be similar up until the 5th hour.
-#(Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
+*(Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
-#(Question 10, p. 118) Go to the Saccharomyces Genome Database 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 change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
+**Most spots would be yellow at the first time point because there was no change in the gene expression. No change in gene expression suggests that the gene was not expressed nor repressed in the cell.
-#(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
 #(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
 #(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?

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 =='''Questions'''==
-#(Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.
+*(Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.
 [[Image:Transcription_Change.jpeg|thumb]]
-#(Question 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, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
+*(Question 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, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
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 |}
-#(Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
+*(Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
 #(Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
 #(Question 10, p. 118) Go to the Saccharomyces Genome Database 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 change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).