Difference between revisions of "Knguye66 Week 9"

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(→‎Methods/Results: add answers and go:gene)
(→‎Methods/Results: add answers (definitions of gene))
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# Look up the definitions for each of the terms at http://geneontology.org. In your research presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?
 
# Look up the definitions for each of the terms at http://geneontology.org. In your research presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?
 
#* Top 6 Gene Ontology (corrected p-value < 0.05): only 7 out of 202 records found, all clustered in Row 28-34.  
 
#* Top 6 Gene Ontology (corrected p-value < 0.05): only 7 out of 202 records found, all clustered in Row 28-34.  
−
#** GO:0000178
+
#** GO:0000178 (exosome, RNase complex): A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured. (Source: PMID:26726035, PMID:17174896, PMID:20531386)
−
#** GO:0070478
+
#** GO:0070478 (nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay): The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction. (Source: PMID:12769863)
 
#** GO:0004004
 
#** GO:0004004
 
#** GO:0030515
 
#** GO:0030515

Revision as of 19:53, 28 October 2019

Microrray Data Analysis (wild type data)

Purpose

This week's assignment is to continue the Microarray Data Anaylsis for wild type data. Step 4 and 5 from Week 9 are featured: Viewing and Saving STEM results, and Analyzing and Interpreting STEM results. For reference and files, go to: knguye66 Week 8.

Methods/Results

After finishing the steps on Week 9 for Viewing and Saving STEM results on stem.jar, screenshots of each profile were placed on a powerpoint (see Data and Files below), and the Profile Gene Table and Profile GO Table list for each table were compressed and zipped into files. Following this step, Profile #45 was chosen to analyze and interpret.

Analyzing and Interpreting STEM Results:

- Profile #45 -

  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose this model expression profile because the average log before t=60 is above the x-axis and after t=60, it is below the x-axis. Of all the colored profiles, Profile #45 has the most significant p-value.
  2. How many genes belong to this profile?
    • 549.0 genes were assigned to this profile.
  3. How many genes were expected to belong to this profile?
    • 47.1 genes were expected to belong to this profile.
  4. What is the p value for the enrichment of genes in this profile?
    • p-value = 0.00 (significant)
  5. How many GO terms are associated with this profile at p < 0.05?
    • 81 of 202 records found.
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 7 of 202 records found.
  7. Look up the definitions for each of the terms at http://geneontology.org. In your research presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?
    • Top 6 Gene Ontology (corrected p-value < 0.05): only 7 out of 202 records found, all clustered in Row 28-34.
      • GO:0000178 (exosome, RNase complex): A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured. (Source: PMID:26726035, PMID:17174896, PMID:20531386)
      • GO:0070478 (nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay): The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction. (Source: PMID:12769863)
      • GO:0004004
      • GO:0030515
      • GO:0000055
      • GO:0032543

Data and Files

Conclusion

Acknowledgements

This section is in acknowledgement to partner Christina Dominguez (User:Cdomin12), as well as, Marcus Avila (User:Mavila9) and Jonar Cowan (User:Jcowan4). I would also like to acknowledge Dr. Dahlquist (User:KDahlquist) for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

User Page

User:knguye66

Template Page

Template:knguye66


Table of all assignments and journal entries for BIO-367-01

Week Individual Journal Entry Shared Journal
Week 1 - Class Journal Week 1
Week 2 knguye66 Week 2 Class Journal Week 2
Week 3 ILT1/YDR090C Week 3 Class Journal Week 3
Week 4 knguye66 Week 4 Class Journal Week 4
Week 5 DrugCentral Week 5 Class Journal Week 5
Week 6 knguye66 Week 6 Class Journal Week 6
Week 7 knguye66 Week 7 Class Journal Week 7
Week 8 knguye66 Week 8 Class Journal Week 8
Week 9 knguye66 Week 9 Class Journal Week 9
Week 10 knguye66 Week 10 Class Journal Week 10
Week 11 knguye66 Week 11 FunGals
Week 12/13 knguye66 Eyoung20 Week 12/13 FunGals
Week 15 knguye66 Eyoung20 Week 15 Class Journal Week 15

References

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