Comparison of hallmark GO biological processes identified as significant in the differential expression of tumorigenic verses normal samples by enrichment of the significant genes called by various the methods. Results of GSEA [15, 30] analysis are included for comparison. Colored boxes indicate that the GO category is identified as significant with an FDR of 10% (60% for GSEA), and deeper red colors have a smaller mean rank of the gene set, corresponding to more up-regulation of the set, while deeper blue colors have a larger mean rank, corresponding to more down-regulation of the set. The GO categories are sub-categorized corresponding to the six hallmark characteristics of cancer as indicated in the inset box. The seventh category is included to evaluate the significance of the hypoxia GO category.