Difference between revisions of "Cdomin12 Week 9"

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(→‎Data & Files: added excel workbook)
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==Methods/Results==
 
==Methods/Results==
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# '''Viewing and Saving STEM Results'''
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## A new window opened called "All STEM Profiles (1)".
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##* Clicked on the button that says "Interface Options...".  At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", clicked on the radio button that says "Based on real time".  Then closed the Interface Options window.
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##*Took a screenshot of this window and pasted it into a PowerPoint presentation to save figures.
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## Clicked on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
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##* Took a screenshot of each of the individual profile windows and saved the images in PowerPoint presentation.
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##* At the bottom of each profile window, there were two yellow buttons "Profile Gene Table" and "Profile GO Table".  For each of the profiles, clicked on the "Profile Gene Table" button to see the list of genes belonging to the profile.  In the window that appears, clicked on the "Save Table" button and saved the file to your desktop.  Made filename descriptive of the contents, e.g. "wt_profile48_genelist.txt".
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##** Uploaded these files to the wiki and linked to them on individual journal page.  (Note that it will be easier to [[Week_4#Compressing_and_Decompressing_Files_with_7-Zip | zip all the files together]] and uploaded them as one file).
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##* For each of the significant profiles, clicked on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile.  In the window that appears, clicked on the "Save Table" button and save the file to your desktop.  Make filename descriptive of the contents, e.g. "wt_profile48_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number.  At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
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##** Uploaded these files to the wiki and link to them on your individual journal page.
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===Profile 48===
 
===Profile 48===
 
====Why did you select this profile? In other words, why was it interesting to you?====
 
====Why did you select this profile? In other words, why was it interesting to you?====

Revision as of 12:42, 30 October 2019

User Page

template: cdomin12

Assignment Page Individual Journal Entries Class Journal
Week 1 cdomin12 Week 1 Class Journal Week 1
Week 2 cdomin12 Week 2 Class Journal Week 2
Week 3 RAD53 / YPL153C Week 3 Class Journal Week 3
Week 4 cdomin12 Week 4 Class Journal Week 4
Week 5 IMG/VR Week 5 Class Journal Week 5
Week 6 cdomin12 Week 6 Class Journal Week 6
Week 7 cdomin12 Week 7 Class Journal Week 7
Week 8 cdomin12 Week 8 Class Journal Week 8
Week 9 cdomin12 Week 9 Class Journal Week 9
Week 10 cdomin12 Week 10 Class Journal Week 10
Week 11 cdomin12 Week 11 Skinny Genes
Week 12/13 Skinny Genes Quality Assurance Skinny Genes
Week 15 Skinny Genes Deliverables Skinny Genes

Purpose

Methods/Results

  1. Viewing and Saving STEM Results
    1. A new window opened called "All STEM Profiles (1)".
      • Clicked on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", clicked on the radio button that says "Based on real time". Then closed the Interface Options window.
      • Took a screenshot of this window and pasted it into a PowerPoint presentation to save figures.
    2. Clicked on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
      • Took a screenshot of each of the individual profile windows and saved the images in PowerPoint presentation.
      • At the bottom of each profile window, there were two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, clicked on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, clicked on the "Save Table" button and saved the file to your desktop. Made filename descriptive of the contents, e.g. "wt_profile48_genelist.txt".
        • Uploaded these files to the wiki and linked to them on individual journal page. (Note that it will be easier to zip all the files together and uploaded them as one file).
      • For each of the significant profiles, clicked on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, clicked on the "Save Table" button and save the file to your desktop. Make filename descriptive of the contents, e.g. "wt_profile48_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
        • Uploaded these files to the wiki and link to them on your individual journal page.






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

Excel Workbook

Week 9 Files

Week 9 Slide

text file for STEM analysis

Transcription Factors

File Uploaded to GRNsight

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

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2019/index.php?title=Cdomin12_Week_9&oldid=5474"