Kmill104 Week 10
Jump to navigation
Jump to search
- Analyzing and Interpreting STEM Results
- Select one of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. Each member of your group should choose a different profile. Answer the following:
- Why did you select this profile? In other words, why was it interesting to you? I chose the 45 profile. This was most interesting to me because it was the most significant profile, and the up-regulation occurs early and then drops.
- How many genes belong to this profile? 549.0
- How many genes were expected to belong to this profile? 47.1
- What is the p value for the enrichment of genes in this profile? 1.00
- Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
- Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. How many GO terms are associated with this profile at p < 0.05? 81
- The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. How many GO terms are associated with this profile with a corrected p value < 0.05? 11
- Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
- cytoplasmic exosome (RNase complex) (GO:0000177)
- nucleic acid binding (GO:0003676)
- ribosomal large subunit export from nucleus (GO:0000055)
- snoRNA binding (GO:0030515)
- mitochondrial translation (GO:0032543)
- nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)
- Each member of the group will be reporting on his or her own cluster in your research presentation. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
- Note whether the same GO terms are showing up in multiple clusters.
- Look up the definitions for each of the terms at http://geneontology.org. In your journal entry, 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)? I'm not completely sure why these specific genes had a change in expression, but I noticed that the genes were concerned with regulating rNA and protein production from mRNA. When cold shock is experienced by the cell, there likely needs to be a change in what mRNA is transcribed and at what rate. Additionally, the formation of proteins and the rate at which they are formed must also be regulated.
- Select one of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. Each member of your group should choose a different profile. Answer the following:
Second question is not related to the wild type strain
- To easily look up the definitions, go to http://geneontology.org.
- Copy and paste the GO ID (e.g. GO:0044848) into the search field on the left of the page.
- In the results page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
- The definition will be on the next results page, e.g. here.
- definition of cytoplasmic exosome (RNase complex) (GO:0000177): A ribonuclease complex that has 3-prime to 5-prime processive hydrolytic exoribonuclease 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.
- nucleic acid binding (GO:0003676): Binding to a nucleic acid.
- ribosomal large subunit export from nucleus (GO:0000055): The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
- snoRNA binding (GO:0030515): Binding to a small nucleolar RNA.
- mitochondrial translation (GO:0032543): The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code.
- nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035) : The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA.
Stopping point for Thursday's lab. Be sure to upload all of the files requested to your Week 10 individual journal entry by 12:01am on Tuesday, March 26 so that the files can be checked before we do the next step on Tuesday. Also invoke your template on your Week 10 individual journal entry right away.
