Functional Analysis Progress Summary
- I struggled with creating the correct significant DEGs vector for the first step. I also did not initially realize that we had to have two separate DEG vectors, for up and down regulated genes. This led to problems while plot the cnetplot. I was able to troubleshoot this issue by going to office hours and consulting my group members.
*In addition, there were errors during the visualization of the GSEA result step. I was able to fix this problem by changing the geneVector.
Summary of work:
- Defined a significant DEG vector and performed EnrichGo analysis for data vitalization through a bar plot.
- Used EnrichKEGG and Enrich DGN to perform pathway analysis- visualized the result using dotplot and cnetplot
- Found Hub genes using the STRING DB database and performed GSEA to analyze hallmark genes
Using the string db database was very interesting. The functional analysis step enabled me to learn the most about the connection of our results to the biological aspect of the paper.