Assignment #6

Singh et al PAPER

DATA FOR ASSIGNMENT 5

A seminal paper published by Singh et al (CELL, 2009) demonstrated that not all KRAS mutant cancer cell lines are "addicted" to this oncogene for survival signaling. Using a series of elegant knockdown experiments in lung and pancreatic cancer cell lines, they showed that KRAS mutant cancer cell lines could be classified as "KRAS-Dependent" and "KRAS-independent" groups. Your assingment is to find the differentially expressed genes in the lung cancer "KRAS-dependent" and "KRAS-independent" using SAM (FDR < 0.1). All data are available here.

Your tasks are:

1. Use NIH DAVID to check the enriched GO categories and KEGG pathways in "KRAS-dependent" group.
2. Use NIH DAVID to check the enriched GO categories and KEGG pathways in "KRAS-independent" group.
3. Use KEGG Search & Color Pathway tool to plot the top 3 pathways enriched in "KRAS-dependent" group.
4. Use KEGG Search & Color Pathway tool to plot the top 3 pathways enriched in "KRAS-independent" group.
5. Run GSEA on this data set and find out the enriched pathways in "KRAS-dependent" and "KRAS-independent" groups. Use this Chip file to collapse the probesets. Use the KEGG gmt file from the GSEA program.

6. Send me the list of GO and KEGG pathways enriched in "KRAS-dependent" and "KRAS-independent" in excel, and the colored KEGG pathways in PPT. List out the GSEA results in "KRAS-dependent" and "KRAS-independent", and check whether the pathways are the same as in NIH DAVID. Put all into a folder, zipped and send.