Icrespin Journal Week 6 - Revision history

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 *References (as shown under References section) were copied from Week's 6 Assignment page.
-*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 20:38, 9 October 2019 (PDT)
+*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 21:01, 9 October 2019 (PDT)
 == References ==

← Older revision		Revision as of 03:55, 10 October 2019
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	LMU BioDB 2019. (2019). Week 6. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_6		LMU BioDB 2019. (2019). Week 6. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_6
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		+	[[Category:Journal Entry]]

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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.'''
-[[File:Crespin_Week6Figure.png|center|400px|]]
+[[File:Crespin_Week6Figure.png|thumb|center|400px|Genes DMC1 and SPS1 are in a graph to show transcription rate using gene induction.
+]]
 *'''(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 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.'''
 [[File:Crespin_Week6Figure.png|center|400px|]]
-**Genes DMC1 and SPS1 are in a graph to show transcription rate using gene induction.
 *'''(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 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.'''
 [[File:Crespin_Week6Figure.png|center|400px|]]
-*Genes DMC1 and SPS1 are in a graph to show transcription rate using gene induction.
+**Genes DMC1 and SPS1 are in a graph to show transcription rate using gene induction.
 *'''(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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 == Acknowledgments ==
 *This week, my homework partner was [https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/User:Imacarae Ivy Macaraeg]. We exchanged phone numbers and discussed for a little while about the objectives of this week's assignment.
 == References ==

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 **The mechanism that the genome could use would be the "guilt by association" method. It consist of two rules that state genes with similar expression profiles should have similar promoters and vice versa. By using this method, it would give information of how similar genes can help predict or discover the unknown ones.
 *'''(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?'''
 *'''(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?'''
 == Acknowledgments ==