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

Figure 4 Comparison of the benign or borderline gastrointestinal stromal tumors (benign and 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: Forty-five percent 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 (BB 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. Fifty-four miRNAs show adjusted P-values (FDR) below 0.1 and fold-changes above 2 (shown in red); D: Hierarchical clustering of the 23 benign or 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.