Difference between revisions of "Cdomin12 Week 9"
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==Data & Files== | ==Data & Files== | ||
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[[Media:Week 9 filesCD.zip|Week 9 Files]] | [[Media:Week 9 filesCD.zip|Week 9 Files]] | ||
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[[Media:BIOL367 F19 microarray-data wt (2)CDupdate1 2.xlsx | Transcription Factors]] | [[Media:BIOL367 F19 microarray-data wt (2)CDupdate1 2.xlsx | Transcription Factors]] | ||
| − | [[Media:RegulationmatrixCD.xlsx | File Uploaded to GRNsight | + | [[Media:RegulationmatrixCD.xlsx | File Uploaded to GRNsight]] |
==Conclusion== | ==Conclusion== | ||
Revision as of 00:04, 30 October 2019
Contents
- 1 Purpose
- 2 Methods/Results
- 2.1 Profile 48
- 2.1.1 Why did you select this profile? In other words, why was it interesting to you?
- 2.1.2 How many genes belong to this profile?
- 2.1.3 How many genes were expected to belong to this profile?
- 2.1.4 What is the p value for the enrichment of genes in this profile?
- 2.1.5 How many GO terms are associated with this profile at p < 0.05?
- 2.1.6 How many GO terms are associated with this profile with a corrected p value < 0.05?
- 2.1.7 Definitions of GO Terms
- 2.1.8 How many transcription factors are green or "significant"?
- 2.1.9 Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
- 2.1 Profile 48
- 3 Data & Files
- 4 Conclusion
- 5 Acknowledgments
- 6 References
Purpose
Methods/Results
Profile 48
Why did you select this profile? In other words, why was it interesting to you?
It has an upward and then downward trend, which I thought would be interesting to investigate at the different time points in how it related to cold shock.
How many genes belong to this profile?
77 genes
How many genes were expected to belong to this profile?
36.7 expected genes
What is the p value for the enrichment of genes in this profile?
2.7E-9
How many GO terms are associated with this profile at p < 0.05?
4 GO terms
How many GO terms are associated with this profile with a corrected p value < 0.05?
2 GO terms
Definitions of GO Terms
GO:0008380:"The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA"
GO:0006397: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide"
How many transcription factors are green or "significant"?
1 is significant
Are CIN5, GLN3, and/or HAP4 on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
Yes, they are all on this list
HAP4
% in user set: 15.79
% in YEASTRACT: 1.10
p value: 0.376430967479230
CIN5
% in user set: 19.74
% in YEASTRACT: 0.69
p value:0.976606065487304
GLN3
% in user set: 46.05
% in YEASTRACT: 1.45
p value: 0.009368736870331
Data & Files
Conclusion
Acknowledgments
1. I worked with User:Knguye66, User:Jcowan4, and User:Mavila9 for this assignment.
2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Cdomin12 (talk) 19:25, 28 October 2019 (PDT)
References
- GeneOntology. Retrieved October 28, 2019 from http://geneontology.org
- Week 9. Retrieved October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
