ArashLari Week 6

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Discovery Questions

Question 1

ArashLariQuestion1BioData.jpg

Question 2

The table's caption
Gene X Gene Y Gene Z
Hour 1 Black Black Black
Hour 3 Dim Red Medium Red Dim Red
Hour 5 Black Black Medium Red
Hour 9 Bright Green Bright Green Medium Red

Question 3

Gene X and Y were transcribed similarly.

Question 4

Most spots would be yellow because there would be equal levels of red and green cDNA, meaning that the gene is transcribed both in the presence and absence of oxygen in the opening reading frame.

Question 5

TEF4 was repressed according to the figure, probably because it needs glucose to help with translational elongation, so when there's less glucose it's less able to do that.

Question 6

Acetyl-CoA enters the TCA Cycle as glucose depletes, therefore the genes would be induced to handle the influx of new molecules and retain energy.

Question 7

If there are genes in a common pathway, they could be induced or repressed simultaneously.

Question 8

I would expect the spots to be red because in the absence of TUP1 the cells would continue to express the gene without the presence of glucose

Question 9

I would expect the spot to be red because Yap1p responds to stress, and glucose depletion is an environmental stress.

Question 10

I would compare them with control variables, and have a large quantity. I would check the red ones for depletion of Tup1 and the bright red ones for over expression of Yap1.

Acknowledgments

  1. I worked with my homework partner Emma Tyrnauer over text. We were available for one another for questions about the assignment.
  2. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

ArashLari (talk) 01:32, 10 October 2017 (PDT)

References

  1. 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.
  2. 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.
  3. Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
  4. Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays
  5. LMU BioDB 2017. (2017). Week 6. Retrieved October 9, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6

Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments


Journal Entries:

Shared Journals:

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