Expression profile of microRNAs in gastrointestinal stromal tumors revealed by high throughput quantitative RT-PCR microarray

Figure 3 Comparison of the borderline gastrointestinal stromal tumors (borderline group) vs the malignant gastrointestinal stromal tumors (M group). A: MA plot of assays used to profile the compared samples: fold-change (Y-axis) vs normalized Ct measurements; B: 45% of the variance observed in the Ct measurements of the 50 most variable (top 50) miRNA assays across all samples can be attributed to the sample description (BO or M). The remaining covariates considered here (“gender”, “tumor grade”, or “stage”) account for less than 5%; C: Volcano plot of the resulting P-values of the t-test between the Bo and M groups. Eighty-two miRNAs show adjusted P-values (FDR) below 0.1 and fold-changes above 2 (shown in red); D: Hierarchical clustering of the 14 borderline GIST tissues and 30 malignant GIST tissues based on the 50 most variable (top 50) miRNA assays. GIST: Gastrointestinal stromal tumor; FDR: False discovery rate; M: Malignant GIST tissues.