Objective

Rank normalized data set from assignment 1 and rank genes by differential expression. Then perform thresholded over-representation analysis to find the major pathways that are enriched or suppressed in my data set.

Duration

Expected duration: 5h Actual duration: 15h

Progress

Tasks

1. Rank genes by differential expression.
2. Perform thresholded over-representation analysis.
3. Interpret the results and write an R notebook.

Differential expression analysis

• I calculated differential gene expression stats using edgeR
• Calculated differential expressions separately for the CPT1A kock-down experiment and the CPT1A over-expression experiment
• Made a volcano plot to visualize results
• Made heat maps for the KD and OE experiments and analyzed clustering of conditions: the control samples are clustered together and the experiment samples are in a different cluster
• Added headings and captions to all figures

Thresholded over-representation analysis

• Made thresholded lists of differentially expressed genes and saved them as text files
• Used G:Profiler to identify processes affected by CPT1A expression

Result interpretations

• See R Notebook: Assignment 2 html notebook
• Added a link to this journal in the notebook

Conclusions and Outlook

• Differential gene expression analysis along with over-representation analysis can be used to identify cellular processes that are up- or down-regulated by the target gene expression.