Differentially expressed genes. (A) Venn diagram of the differential expression results for the comparisons among nevi, melanocytes and melanoma Green circle, the number of genes with different expression levels between nevi and melanocytes. Yellow circle, the number of genes with different expression levels between melanoma vs. nevi. Orange circle, the number of genes with different expression levels between melanoma vs. melanocytes. Colors in the Venn diagram match the color of each comparison shown in B. (B) Diagram illustrating how the expression of genes change as they follow a path that ultimately results in melanoma. Blue and red lines indicate downregulation and upregulation, respectively. Black lines indicate no change. Genes in samples that developed melanoma directly from melanocytes are shown in the top panel, and the number of genes that was used to assess changes is indicated. Genes in samples in which melanoma developed from an intermediary nevus are shown at the bottom, and the number of genes that was used to assess changes from nevus to melanoma are indicated. As indicated in this diagram, 3 possible paths were identified in melanoma samples that had directly transformed from melanocytes, and 9 possible paths were identified in melanoma samples that transformed via an intermediary nevus. A given gene may have 10 possible transformation paths at the transcriptome level when removing the 2 paths that did not show changes in expression. (C) Hierarchical clustering based on the 50 most discriminating genes that are unique to each comparison: Melanoma vs. melanocytes (2,331 genes) and melanoma vs. nevi (888 genes). Melanocyte (light green label), nevus (dark green label) and melanoma (yellow label) samples fell into two major groups. (D) Hierarchical clustering based on the 50 most discriminating genes that are common to each comparison: Melanoma vs. melanocytes and melanoma vs. nevi (682 genes). Melanocyte (light green label), nevus (dark green label) and melanoma (yellow label) samples fell into two major groups.