Fig. 5

Representative RBP groups correlated with RNA degradation and splicing data. a Known physical interactions between RBPs in Group 9. b We calculated the fractions (log2 ratios) having binding sites co-bound by Group 9 (or binding peaks identified from individual RBP’s CLIP-seq data) for long half-life genes and short half-life time genes. The binding peaks of single RBP are the overlapped ones defined by both Piranha and PARalyzer using default parameters. The average and standard deviation of the ratios for individual RBPs are shown. The enrichment was tested with Fisher’s exact test for each individual RBP and the group, respectively. Four numbers were used in the test: total number of long half-life genes, total number of short half-life genes, numbers of long and short half-life genes containing the binding sites/peaks. (***p value < 0.001). c A group-related binding site located at 3′-UTR of gene MARCH9 with short half-life. d A single RBP’s binding site located at 3′-UTR of gene IPO8 with long half-life. e, h Known physical interactions between RBPs in groups 4 and 6. f, i We calculated the fractions (log2 ratios) having binding sites co-bound by RBPs in group 4/6 (or binding peaks identified from individual RBP’s CLIP-seq data) for AS exons and constitutive exons. The average and standard deviation of the ratios for individual RBPs are shown. The enrichment was tested with Fisher’s exact test for each individual RBP and the group, respectively. Four numbers were used in the test: total number of AS exons, total number of constitutive exons, numbers of AS and constitutive exons close to the binding sites/peaks. (**p value < 0.005; ***p value < 0.001). g, j Group 4/6 associated binding site, which is located near cassette exon(s) of gene LUC7L2/TCF7L2 with low PSI score. The binding site of group 4 contains the known motif, UGUGU