Class Journal Week 10
Katie Miller
What aspect of this assignment came most easily to you? I found STEM and YEASTRACT both relatively easy to use whenever I followed the steps exactly as written in the procedure. The YEASTRACT section was the most straightforward and easy for me to complete.
What aspect of this assignment was most challenging to you? I had trouble constructing my Gene Regulatory Network, which was because my first several attempts always had some gene being left out and not connected to any others, so I had to go back and restart the process. I also had some trouble narrowing down my 6 gene ontology terms, because I wanted to make sure I didn't use terms that had very similar meanings.
What (yet) do you not understand? I don't really understand what impact the deletions of CIN5 or GLN3 will have on the results because I have been analyzing the wild type data. I'm excited to see how this affects the yeast response and its gene regulation. In terms of wiki skills, I still don't understand how to save files under the same name so that the multiple versions are stored in our wiki.
Kmill104 (talk) 23:51, 3 April 2024 (PDT)
Hailey Ivanson
What aspect of this assignment came most easily to you?
I found the data-driven parts of this assignment to be easy; calculations on Excel, especially when there are instructions, are intuitive for me.
What aspect of this assignment was the most challenging for you?
Aside from my weird and brief struggle with STEM, making the GRN using GRNsight was not a terrible challenge, but I found it to be tedious. Entering and re-entering all of the transcription factors with some slight modifications/additions/removals for each new GRN took me almost a whole class period.
What (yet) do you not understand?
I'm not sure I completely understand what the deletion of CIN5 transcription factor does with respect to cold shock. I know that it has a role in oxidative stress response pathways in yeast, but I don't know what the expected outcomes would be given this information. I also don't completely understand the language surrounding GO terms and definitions; I don't really understand the difference between terms and .
Hivanson (talk) 22:38, 3 April 2024 (PDT)
Charlotte Kaplan
- What aspect of this assignment came most easily to you?
Selecting GO terms and adjusting the p-values for profile 45 was relatively easy because it involved straightforward filtering in Excel to identify significant terms. After filtering, finding definitions for the selected GO terms was also straightforward using the Gene Ontology website, as it only required copying and pasting the GO IDs into the search field. Overall, this aspect of the assignment involved less technical manipulation in Excel and more direct interpretation of biological significance, making it easier to accomplish for me.
- What aspect of this assignment was the most challenging for you?
The most challenging part of the assignment was preparing the microarray data file for loading into STEM. This involved several steps I was unfamiliar with, including filtering the data based on the Benjamini-Hochberg corrected p-value, deleting rows with insignificant changes in expression, deleting unnecessary data columns, and addressing any remaining #DIV/0! errors. Additionally, saving the file in the correct format posed some difficulty, especially considering the need to turn on file extensions if not already enabled. Before this assignment, I had little to no experience with excel and Andrew helped me figure a lot out.
- What (yet) do you not understand?
I still don't feel 100% comfortable doing this in excel by myself. Having the help of Andrew (my homework partner), Dr. Dahlquist, and my peers helped me a lot.
