Fig. 3: Functional phenotypic and genotypic effects of the miR-302 super-family-inhibitor (miR-302-SFI) in malignant GCT cells.
a Cell numbers for TCam-2 (Sem; upper panel), 1411H (YST; central panel), and 2102Ep (EC; lower panel) at day 7 in untreated cells, mismatched control (MMC), and miR-302-SFI-treated cells. Key: **p < 0.01; ns = not significant. b Sylamer landscape plots for TCam-2 (upper panel), 1411H (central panel), and 2102Ep (lower panel) cells treated with miR-302-SFI, compared with MMC, at day 2 post-transfection. Log10 transformed, sign-adjusted enrichment p values for each seed complementary region (SCR) ‘word’ relative to all other words are plotted on the y-axis against the ranked gene list on the x-axis, which has upregulated (de-repressed) genes to the left and downregulated genes to the right. SCRs corresponding to true miRNAs (as listed in miRBase version 22.1) that reach significance by extreme value distribution and which correspond to the AAGUGC seed sequence are shown in colour; their p values are listed in the top right of the graph. Non-significant word plots are shown in grey. The change point detection value (CPDV) algorithm was used to determine the most appropriate Sylamer enrichment peak for selecting gene lists for further analyses. The bin with the maximum CPDV was selected and indicated by the vertical dotted line; this represented bin 8 (1600 genes) for both the TCam-2 and 1411H cell lines.
