Fig. 2.

Gene set testing of K14E7 ‘UP’ and ‘DOWN’ gene signatures in human CIN3 versus CIN1/CIN2 and cervical cancer versus CIN3. (A-B) GSEA analysis of (A) CIN3 versus CIN1/CIN2 or (B) cancer versus CIN3 of K14E7 ‘UP’ or ‘DOWN’ signatures. Ranking of genes in the ‘UP’ gene signatures (red) or ‘DOWN’ gene signatures (blue) are shown at the bottom of each GSEA plot. Position and frequency of genes contributing the most to each enrichment are highlighted in orange. (C) Barcode enrichment plot of t-statistic ranked genes from LIMMA for CAMERA gene set testing. The enrichment value corresponds to the relative ‘weight’ value in LIMMA. (D) ROAST gene set testing of CIN3 versus CIN1/CIN2 or cancer versus CIN3. Proportion of genes corresponding to up or down regulated and assigned direction and p-value are shown. Genes are assigned to the up or down bins according to the probability formula specified in ROAST. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)