Fig. 5

Validation of the co-expression derived networks using RAT assay. a, b Box plots of the odd ratios (a) and p values (b) of overlap between co-expression networks and the chromatin interaction datasets after stratifying the genes into the top and bottom half based on the expression. c Top: definition of the odds ratio and the depiction of the hypothesis tested in the part below. Bottom: box plots of the odds ratios of the overlaps between the co-expression networks and genes containing RAT regions at the gene (left) and region (right) levels at different RAT signal thresholds (X-axes). d A diagram illustrating selection of final RAT signal thresholds for each of the 14 vlincRNA-treatment combinations based on the best overlap with the co-expressed genes. e, f Overlap between the co-expression networks and genes containing RAT signals at the final RAT signal thresholds for the SMS and Illumina platforms. Odds ratios (e) and p values (f) are shown