Figure 3

Evaluation of direct miRNA regulation of target mRNAs using in vitro transfection data. A. Heatmap showing inverse expression patterns between miR-16 and its 191 targets (module # 4 in Table 2). Top row shows miR-16 expressions across 30 liver biopsy samples, rows below for its targets. Columns represent samples, identical for both miRNAs and mRNAs. Expressions converted into z-scores. Entry in yellow (blue) indicates expression level of a gene is higher (lower) than mean across all samples. B. Heatmap showing down-regulation of miR-16 targets after transfection into cultured cells. Rows are targets and columns are experiments. The measurements for 181 of 191 targets available, and shown as log2 ratios of 24 h after transfection to mock. Transfections were done with 100 nm miRNAs using HCT116 Dicer-/- cells, the first with 25 nm miRNAs using DLD-1 Dicer -/- cells. In table at the bottom, row 'Mis_match' shows if miR-16 with mismatches used, indicated by locations. 18,19 represents mismatches at positions 18 and 19 of miR-16 mature sequences counted from 5'. 18,19 and 19,20 (2,3 and 4,5) outside (within) seed region. One-sample t-tests (Pval.t for p-values) and non-parametric Wilcoxon tests (Pval.wc) used to assess if overall target expressions shifted after transfection. C. Heatmap showing inverse expression patterns between miR-215 and its 86 targets (module #27 in Table 2), similarly as in (A). D. Heatmap showing down-regulation of miR-215 targets after transfection, similarly as in (B). The measurements for 85 of 86 targets were available. Table at the bottom shows cell types (Cell) and concentrations ('Conc.'). The transfection data was downloaded from GEO: GSM156550, GSM156546, GSM156565, GSM156566, GSM156563, GSM156564 for data shown in (B) from left to right, and GSM156552, GSM156548 in (D). See Linsley et al, 2007 for details.