In this section, we give three examples that illustrate different aspects of the use of the hallmark collection for GSEA. The first example shows how using only the hallmarks can form the basis for a concise and sensitive comparison between subtypes of medulloblastoma. It also illustrates the type of summarization that hallmarks provide for their founder sets. The next example necrosis in glioblastoma, demonstrates the redundancy reduction gained from using the hallmark collection instead of the original MSigDB collections C1 – C6. Finally, in the last example we show that hallmarks can effectively associate with their corresponding protein activation phenotypes thus confirming their biological relevance.
