Figure 1

Identification of antagonistic miRNA clusters using the NCI60 data sets. (A) Correlation of gene signatures with 136 miRNAs grouped into 13 miRNAs clusters according to their positively correlating genes as recently described [4]. Left panel, average EMT gene signature (see Methods). M, mesenchymal genes; E, epithelial genes. Right panel, c-Myc-repressed (repr.) and c-Myc-induced (ind.) genes. Three clusters that had highly significant correlations in the Wilcoxon rank analysis (p < 10^-7) are highlighted in different colors. The X-axis displays a factor that indicates the level of correlation with the gene sets as explained in the Method section. (B) PCA (Principal Component Analysis) of the 136 miRNAs in A. The miRNAs identified in the three clusters are circled in similar colors as in A. (C) Correlation network based on miRNA groups and gene signatures (E genes, M genes, and oncogenic signatures). Only correlations that were found in the analysis of positively and negatively correlating genes are shown (see Additional file 4: Table S4 and Additional file 6: Table S5). Red box, epithelial; blue box, agonistic; green box, mesenchymal and antagonistic. miRNAs: red, miR-200 family; blue, miR-17 family; orange, other EMT-related miRNAs recently identified [4] (miR-7, miR-203, and miR-375). EMT genes: light green box, E genes; light red box, M genes. Oncogenic signatures: light green, positively correlated with agonistic miRNAs; light red, negatively correlated with agonistic miRNAs. Epithelial specific miRNAs are highlighted in red and members of the miR-17 family of miRNAs are highlighted in blue.