asfarlathif
commented
1 year ago Hi Team Zinc
I will be the TA mentor for your group project. Great presentation! Here is some feedback regarding your proposal lightning talk
Background/Motivation: I like the idea of building on an already published study. It gives you a good foundation to start your analysis to start on. I would have liked to see more about what the study has found and a little more detail on the approaches they used to arrive at their result.
Question/Hypothesis: The above will now help you solidify your research question/ hypothesis. With a lack of overview of the study's findings and approaches it is hard to comprehend how your analysis will be different from the original study and how it will add to their findings. Please make sure to clarify the differences in your written proposal.
Data: Great job on describing the dataset. In your written proposal I would encourage you to include how you might break up the dataset for your newly formed hypothesis.
Analysis: Great plan to begin with. I also agree with Keegan on including both the T2D and obese phenotypes in your linear modelling. That will definitely give you more insights into the relationship between the two conditions.
Here are averaged scores :
| Component | Grades |
|---|---|
| Background/Motivation | 0.625 |
| Question/Hypothesis | 1.5 |
| Data | 0.75 |
| Analysis | 1 |
| Total | 3.875 |
Hi Team Zinc!
I'll be your faculty mentor for this project. I'd like to share some feedback on your lightning talk today to help you prepare your written proposal. Your TA mentor will also provide feedback, along with the results of our combined marking scores.
Intro/motivation: Nice summary of the key findings in the Segerstolpe et al. paper. Could benefit from a brief overview of what is already established about the link between T2D and obesity to further motivate the proposed investigations into the gene expression patterns.
Question/hypothesis: I appreciate your skeptical approach to the previous results, and desire to build upon them. More broadly, your research question and expectations seem to imply that the underlying disease mechanism (as regulated by gene expression) differs for T2D patients that are obese compared to T2D patients who are not obese - in your written proposal, please clarify if this is so. I think this is a very interesting question, but your written proposal should also provide some additional context/background on what is already known regarding these two types of T2D patients - this will also be helpful in interpreting your results.
Data: Great job explicitly defining how your approach is different than that taken by the original study. It is not clear whether the dataset you presented will allow you to answer your research question, however - in particular, it is important to check how many samples had T2D and were not obese, as well as how many healthy samples were obese. I suspect that these two subgroups may be more limited. If you find yourself needing to look for alternative datasets, it could be worthwhile to consider mouse data as there are mouse models of T2D and that data tends to be more abundant/freely available compared to human.
Analysis: Great start! In addition to looking at overlap of differentially expressed genes in the independent comparisons of obesity and T2D, it may be worthwhile to explore a linear model that includes both factors, as well as their interaction (provided you have sufficient sample size in each group). The interaction in particular seems relevant to your question, as it would allow that a gene expression difference associated with T2D can be different for obese and non-obese patients.