Statistical assessment of MSigDB gene sets in colon cancer

Gene expression profiling offers a great opportunity for understanding the key role of genes in alterations which drive a normal cell to a cancer state. A deep understanding of the mechanisms of tumorigen- esis can be reached focusing on deregulation of gene sets or pathways. To this end, we measure the amount of deregulation and assess the statistical significance of predefined pathways belonging to MSigDB collection in a colon cancer data set by using two known and statistically well founded methods. Our study highlights the importance of using gene sets for understanding the main biological processes and pathways involved in colorectal cancer. Our analysis shows that many of the genes involved in these pathways, although obtained in studies on different cancer diseases, are strongly associated to colorectal tumorigenesis.