Fig. 1.

Promoter activities in lung cancer. (a) An MDS plot. Similarities (distances) between individual carcinomas in the space of promoter activities (CAGE profiles) are visualized in two dimensions by the multi-dimensional scaling implemented in the edgeR [20], where individual dots represent individual carcinomas and similar carcinomas are plotted closely. The dot colors represent carcinoma subtypes as indicated in the legend, and the dotted line indicates groups of carcinomas. (b) An MA-plot of the differential analysis between PDSCC and non-lepidic AD. The X-axis represents the average expression levels in cpm, and the Y-axis represents the fold-changes in the log2 scale. Individual dots represent the activities of individual promoters, and the blue dots indicate promoters with statistically significant differences (fold-change > 4, CPM > 4 and FDR < 0.01), and the red dots indicate the marker candidates we selected