Mavila9 Week 9

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User Page

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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

In this section of the investigation, the gene expression profile 9 from the STEM results were selected to further analyze. The profile 9 genes showed initial decreases then increase back to normal expression over time in response to cold shock. It is thought that the profile 9 genes share the same expression pattern because they are regulated by the same transcription factors. YEASTRACT is used to prepare the profile 9 data to form a gene regulatory network of transcription factors using GRNsight. This network can be used to find association between regulation of genes in response to cold shock.

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

GRNsight. Retrieved October 29, 2019, from https://dondi.github.io/GRNsight/ .

Short Time-series Expression Miner (STEM). Retrieved October 29, 2019, from http://www.cs.cmu.edu/~jernst/stem/ .

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

YEASTRACT. Retrieved October 29, 2019, from http://www.yeastract.com/formregmatrix.php .