Biomarkers II: HER2 Gene Set Enrichment Analysis

by Madeline Barry and Lauren Driscoll

Part two of the biomarker project involved a lot of discovery and working through challenges. This project was a continuation of the first part of the biomarker project, where we analyzed a breast cancer dataset and discovered an interesting overlap in the HER2 positive and HER2 negative groups that we wanted to explore further. A general outline was supplied, including a skeleton code that would produce relevant material to put into a Gene SetEnrichment Analysis tool. Our goal was to use the GSEA tool to learn more about what the overlap in groups consisted of, such as if any interesting genes were upregulated or downregulated. Although as a whole this could be perceived as an intimidating project, we were able to work through it by taking it piece by piece. We broke it down into manageable parts that we would figure out, and once we felt comfortable with that particular aspect of the project, we moved on to the next task. This approach proved to be an effective way to navigate through the project and successfully reach milestones.

Technically, one of us was familiar with coding, and the other was not experienced in code, so we could work together to interpret and utilize the code written to analyze our biomarker dataset further. We practiced critical thinking and worked through roadblocks in using GSEA, as we had never used it before. We spent a lot of time attempting to manually enter our dataset and adjust the parameters accordingly, and eventually were able to run our data set successfully. This was probably the most time-consuming aspect, and in retrospect, we could have asked for further assistance. However, it was beneficial to be able to work through it on our own and tackle the challenge. We were able to get a better understanding of how GSEA functions, compared to if we were able to just plug in the dataset and not have to research the purpose behind utilizing each of the parameters.

Read the full report here.