Mavila9 Week 9

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Revision as of 21:08, 30 October 2019 by Mavila9 (talk | contribs) (→‎Methods & Results)
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Links

User Page

Template:mavila9

Assignment Page Individual Journal Entry Class Journal Entry
Week 1 Week 1 (User page) Shared Journal Week 1
Week 2 Mavila9 Week 2 Shared Journal Week 2
Week 3 Gene Page Week 3 Shared Journal Week 3
Week 4 Journal Entry Page Week 4 Shared Journal Week 4
Week 5 RNAct Database Page Week 5 Shared Journal Week 5
Week 6 Journal Entry Page Week 6 Shared Journal Week 6
Week 7 Journal Entry Page Week 7 Shared Journal Week 7
Week 8 Journal Entry Page Week 8 Shared Journal Week 8
Week 9 Journal Entry Page Week 9 Shared Journal Week 9
Week 10 Journal Entry Page Week 10 Shared Journal Week 10
Week 11 Sulfiknights Team Page Shared Journal Week 10
Journal Entry Page Week 11
Week 12/13 Journal Entry Page Week 12 Shared Journal Week 11
Week 12/13 Sulfiknights DA Week 12/13 Shared Journal Week 12
N/A Sulfiknights DA Week 14

Purpose

This investigation serves to further analyze the results from running the STEM program on the gene expression change data after cold shock.

Methods & Results

Steps were followed according to Week 9 Assignment page.

Part 1

  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose this profile because it was statistically significant and included a decrease in expression.
  2. How many genes belong to this profile?
    • 200 genes are assigned to this profile.
  3. How many genes were expected to belong to this profile?
    • 60.3 genes were expected to belong to this profile.
  4. What is the p value for the enrichment of genes in this profile?
    • 3.1x10(^-48) is the p-value for the enrichment of genes in this profile.
  5. How many GO terms are associated with this profile at p < 0.05?
    • 28 GO terms are associated with this profile at p < 0.05.
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 3 GO terms are associated with this profile at p < 0.05.
  7. GO:0000139 definition:
    • Golgi membrane
  8. GO:0006888 definition:
    • endoplasmic reticulum to Golgi vesicle-mediated transport
  9. GO:0015031 definition:
    • protein transport
  10. GO:0005794 definition:
    • Golgi apparatus
  11. GO:0002181 definition:
    • cytoplasmic translation
  12. GO:0005737 definition:
    • cytoplasm

Part 2

  1. How many transcription factors are green or "significant"?
    • 11 transcription factors are green
  2. Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
    • CIN5 is 16% in user set, 1.47% in YEASTRACT, and has a p-value of 0.999998732.
    • GLN3 is 31.5% in user set, 2.6% in YEASTRACT, and has a p-value of 0.729017447.

Data

Microarray data .xlsx

YEASTRACT .xlsx

genelist .xlsx

GOlist .xlsx

STEM - GRNsight results .pptx

Conclusion

Part 1

  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose this profile because it was statistically significant and included a decrease in expression.
  2. How many genes belong to this profile?
    • 200 genes are assigned to this profile.
  3. How many genes were expected to belong to this profile?
    • 60.3 genes were expected to belong to this profile.
  4. What is the p value for the enrichment of genes in this profile?
    • 3.1x10(^-48) is the p-value for the enrichment of genes in this profile.
  5. How many GO terms are associated with this profile at p < 0.05?
    • 28 GO terms are associated with this profile at p < 0.05.
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 3 GO terms are associated with this profile at p < 0.05.
  7. GO:0000139 definition:
    • Golgi membrane
  8. GO:0006888 definition:
    • endoplasmic reticulum to Golgi vesicle-mediated transport
  9. GO:0015031 definition:
    • protein transport
  10. GO:0005794 definition:
    • Golgi apparatus
  11. GO:0002181 definition:
    • cytoplasmic translation
  12. GO:0005737 definition:
    • cytoplasm

Part 2

  1. How many transcription factors are green or "significant"?
    • 11 transcription factors are green
  2. Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
    • CIN5 is 16% in user set, 1.47% in YEASTRACT, and has a p-value of 0.999998732.
    • GLN3 is 31.5% in user set, 2.6% in YEASTRACT, and has a p-value of 0.729017447.

Acknowledgements

I'd like to thank User:Knguye66, User:Jcowan4, and User:Cdomin12 for helping with this investigation. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Mavila9 (talk) 14:55, 29 October 2019 (PDT)

References

Week 9. Retrieved October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9 .

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