- Links for Classroom Practice -

Lecture 13 (3/18)

A. Observe DEGs identified by CuffDiff

1. Link to HiPerGator with Globus , navigate to your CuffDiff results folder (Wholegut_aging).
2. Download the "gene_exp.diff" file to the corresponding folder on your laptop.
3. Open the file in MS Excel and save as a .xlxs workbook file.
4. Extract significant DEGs(differentially expressed genes) with q less than 0.01.
5. separate genes increased in old guts from those decreased.

• Explanation of the difference between p value and q value

B.) Functional interpretation of HTS (RNA-Seq) data

• What is Gene Ontology ? Example of GO:0045087 Innate immune response .
• Inspect "Tree view", "Graph view", and "Annotation".
• What is Enrichment analysis ?
• Practice Enrichment analytsis with g:profiler . Example gene list - Aging_Inc_list generated with Cuff_Diff.

Links used for previous classes.