Difference between revisions of "Emilysimso Week 7"

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==Part One==
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# (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) 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 in hard copy and turn it in in class.
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* Opened up the spreadsheet for the first time
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#* Please see the attached [[File:Simso Week 7 Q1.xlsx|Xcel file]]
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** Taken from [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Minds Part 1]
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# (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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* Scaled and centered the data
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#* X: 1 - black, 3 - dim red, 5 - dimmer red, 9 - dim green
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** It was important to always reference back to the same rows using a dollar sign symbol attached to B2 and B3 (becoming B2$ and B2$) because we want to always compare the other call to these numerical values.
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#* Y: 1 - black, 3 - red, 5 - bright green, 9 - dim green
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* Performed statistical analysis on the data (averages, StdDev, Tstat, Pvalue, Bonferroni Pvalue)
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#* Z: 1 - black, 3 - red, 5 - bright green, 9 - bright green
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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?
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#* Genes X and Y were transcribed similarly, as they both started as emitting more red light and then moved to green as time passed
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# (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?
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#* A yellow color appears when there has been no change in gene expression. Therefore, it makes sense that many of the genes would be yellow at the first time point, as they haven't had time to express the genes.
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#* In the experiment, many of the genes would be yellow because the genes remained the same.
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# (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).
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#*
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# (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
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# (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
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# (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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#*
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# (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?
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#*
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# (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?
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#*
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{{Template: Esimso entries etc}}

Revision as of 00:38, 19 October 2015

  1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) 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 in hard copy and turn it in in class.
  2. (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.)
    • X: 1 - black, 3 - dim red, 5 - dimmer red, 9 - dim green
    • Y: 1 - black, 3 - red, 5 - bright green, 9 - dim green
    • Z: 1 - black, 3 - red, 5 - bright green, 9 - bright green
  3. (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?
    • Genes X and Y were transcribed similarly, as they both started as emitting more red light and then moved to green as time passed
  4. (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?
    • A yellow color appears when there has been no change in gene expression. Therefore, it makes sense that many of the genes would be yellow at the first time point, as they haven't had time to express the genes.
    • In the experiment, many of the genes would be yellow because the genes remained the same.
  5. (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).
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
  7. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
  8. (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?
  9. (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?
  10. (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?

Weekly Assignment Information

User: Emilysimso

Assignments

Individual Journal Entries

Class Journal Entries

Group Project

Heavy Metal HaterZ

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