Assignment 3: Data set Pathway and Network Analysis

Objective

Your task is to take the ranked data that was created in Assignment #2 and perform non-thresholded pathway analysis. Once you performed pathways analysis you summarize and visualize your results using Cytoscape and the Enrichment map pipeline.

Duration

Time estimate: 10h; taken: 20h
Date Started: 2023-04-03; completed: 2023-04-04

Procedure

• GSEA
  • Performed pre-ranked analysis
    • Used the same gene set from the GSEA homework (from Bader lab)
    • I noticed that I didn't include gene names in my ranking but instead used my ENSEMBL ids so went back to the code to fix that and recreate the rankings file
• Cytoscape
  • Using the results from GSEA, I moved onto Cytoscape, and downloaded EnrichmentMap and AutoAnnotate (which took many clicks and attempts to download for some reason) Apps
  • EnrichmentMap created a HUGE network, so I just moved on
  • AutoAnnotate was used, I didn't feel like the cluster annotations were the most accurate

Conclusion and Outlook

Final assignment done!