First complete: MODULE 6 LAB Bioinformatics Part 2: Cancer Gene Expression, Epigenetics & RNA-seq
Part A: Understanding Epigenetic Terms (25 pts)
Answer the following briefly in your own words (1-2 sentences each):
- CpG Island (5 pts)
- CpG Shores (5 pts)
- CpG Shelves (5 pts)
- Open Sea regions (5 pts)
Briefly explain how methylation in these regions typically impacts gene expression. (5 pts)
Part B: Data Preparation (10 pts)
In Excel, import the RNA-seq file (COLO829_expression.xlsxDownload COLO829_expression.xlsx) and methylation files. Take a screenshot that clearly shows the first 10 rows of each imported dataset. (10 pts)
Merge the expression data with methylation data (COLO829_methylationDownload COLO829_methylation) by gene name. Provide a screenshot of the merged table (first 15 rows). (5 pts)
Part C: Expression-Methylation Correlation (20 pts)
Using Excel, create a scatter plot comparing gene expression (log2 TPM) and methylation percentage at TSS (within 1kb) for COLO829. Include a linear trendline and R² value. Paste the plot here. (10 pts)
Describe the correlation observed (strength, direction). Is this expected? Explain in 2-3 sentences. (10 pts)
Part D: Analysis of CpG Regions (20 pts)
Using Excel filters, identify and list 5 genes highly methylated (>75%) in CpG islands and having low expression (bottom 25% TPM) in COLO829, and 5 genes that are lowly methylated and have high expression. Paste your filtered lists here. (10 pts)
Briefly reflect (3-4 sentences): Are these relationships (high CpG island methylation and low gene expression and vice versa) expected biologically? Why or why not? (10 pts)
Part E: Comparison with Control Cell Line (25 pts)
Compare methylation levels in COLO829 with the fold change of the expression levels of the top 5 genes with a positive (higher expression in COLO829) and negative (lower expression in COLO829) fold changes compared to healthy skin. In which group would you expect to find TSGs and oncogenes? How do you think the methylation values would differ in healthy skin? Briefly explain your observations. (25 pts)