BIOL388/S19:Class Journal Week 7
1. If I had to do this project over, I would organize my figures, tables, and screenshots better so that they are easier to find when creating the Powerpoint presentation. I would keep using the Gene Ontology source to look up terms, as it was useful to see the bigger picture of how these gene regulations functionally impact the yeast cells.
2. If I were to continue this project, I would test all of the significant profiles to see if they produce the same phenomena that's seen in my in silico experiment. It didn't occur in my homework partner's profile, so I'd like to see if there is any type of pattern there.
- If you had to do this project over again, what would you do differently? What would you keep the same?
- If I was doing this project again, I would choose a different in silico experiment, as our fixed b model did not return any interesting results. However, besides this, I would choose to keep the rest of the project the same because I did not encounter any real problems.
- What future directions would you take if you were to continue this project as it stands now?
- I think it would be interesting to look at my profile in more depth, specifically extending the model to include time points past 60 minutes. I would choose to do this because the cluster that I chose showed a significant change in expression after 60 minutes when the yeast was in the cold recovery period.
- I would choose a profile that had more activity during cold shock since this project focused on cold shock. My profile had more activity with recovery, so my GRNsight results (which genes and how strongly activated/repressed) look much different than my partners.
- Our tweak to fix the threshold b parameter did not do much to our results. Future directions would include cold shock recovery for the GRNmap workbook. This could either be including all of the timepoints or just doing the recovery timepoints (90, 120).
- If I were able to redo this project, I would choose a different in silico experiment, as removing ZAP1 did not provide many differences. It would be interesting to include the recovery time points as my partner did to have a better comparison. It may also be more efficient to find software to run the ANOVA tests automatically, as opposed to the manual version we did in Excel.
- Moving forward, it would be interesting to look at the individual genes suspected of regulating cold shock. I am also interested in stress granules (or p-bodies which I believe is what to be known to form in yeast), so it would be interesting to see if there were any genes/TF's in any of the profiles that regulate the formation p-bodies in yeast.
- If I were to do this assignment over again, I would keep the same protocol for the beginning part of the experiment and also use the same data analysis techniques; however, I would be interested to test one of the mutant types rather than the wild type to see if there is a bigger change in data when comparing the multiple strains.
- If I were to continue testing the wild type, I would try to test more of the gene profiles that showed more significant changes in activation/repression.
- If I conducted this assignment over again, I would most likely choose a different profile that had more activity throughout the actual cold shock period, rather than recovery. I would also be interested to pick the same genes as my partner and see if there were any similarities in our profile networks.
- A future direction could be to try running the t0-t60 timepoints separate from the t90-t120 timepoints. I think this would help make a clear distinction between cold shock and recovery.
If I had to do this project over again, I would work on keeping my files more organized and create folders for each portion. Organization and finding things was honestly a bit problematic for me during this experiment. I would keep utilizing gene ontology as that resource was helpful. In the future, I would use the list of genes and what in the cell they do, such as protein assembly etc and further look into the genes that had similar functions. Avalekander (talk) 20:08, 9 May 2019 (PDT)