TRM reproducibility of intra- and inter- datasets. The percentage of overlapping genes is calculated as the ratio for the number of intersection and union of the genes. We compared the percentage of overlapping genes on TRM, TRG with the equal number of genes in TRM, and their corresponding permutation test controls (TRM_P and TRG_P). We performed the above comparison on (A) two randomly split halves of Lin07, (B) two datasets for the different microarray platform, van02 and wang05. We compared our overlapping percentage of inter-datasets (orange) with others methods (blue) (C).