Final Project- Meenoti Thakore

Final Project Progress Summary

Presentation:
https://docs.google.com/presentation/d/1rZ6PAX5mM6tXuYB37jRPhOXbSpV1kaFuSzpdkvfV5xg/edit?usp=sharing

Challenges faced:

  • At first, I had to change the data set I was using a few times because there were some problems during the quality control step. However, this was resolved with some trial and error and the rest of the process went pretty smoothly.
  • I spent some more time understanding the biological aspect of the data to give an in- depth explanation during the presentation

Summary of work:

  • Conducted quality control using packages like simpleaffy, and arrayquality metrics to identify outliers
  • Removed the outliers from the downloaded data set plotted PCAs to confirm these results
  • Got the metadata using the instructions from google drive
  • Annotation and gene filtering which removed the NA and low expression genes
  • Conducted analysis with limma and plotted Volcano plots and Heatmaps- wrote the top 100 DEGs into a file
  • Defined a significant DEG vector and converted the gene symbols into gene IDs
  • Performed EnrichGO, EnrichKEGG, and EnrichDGN analysis and visulaized the results into a barplot, cnet plot, and dotplot
  • Performed GSEA analysis to analyze hallmark genes
  • Created a presentation using some of the results

Further notes:
For the final presentation, I identified which plots would be most effective to use and explain. I did research on those specific plots and found how they related to colorectal cancer and the data set I used. Since the presentation was a little longer than the normal weekly presentations, I was able to go in-depth about certain biological signaling pathways related to colorectal cancer.

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