Pathway analysis based on the log2 fold change for clusters 1 and 4 compared to normal.

Fold change level of molecules involved in antigen processing and presentation molecules in cluster 1 (A) and cluster 4 (B). Fold change level of molecules involved in leukocyte recruitment in cluster 1 (C) and cluster 4 (D). These results show how cluster 1 genes for the first 2 steps of the cancer-immunity cycle are up-regulated while those of cluster 4 are mostly downregulated. These pathways and others for other clusters and steps of the cancer-immunity pathway are in S5 File. The color scale ranges from the downregulated expression in green (-1 fold), to the non-differential expression in grey, to the up-regulated expression in red (+1 fold).