Fig. 7

Properties of vlincRNA regulatory networks. a Stability of the regulatory networks in different treatments—box plots of the odds ratios of the overlap between networks in the DMSO- and drug-treated samples for the 6 vlincRNAs. b–e Regulation of multiple genes in trans and cis. Most of the genes in the positively and negatively correlating networks are found on different chromosomes as illustrated for the co-expression networks of the vlincRNA ID-1202 in either etoposide or DMSO treatments. Connections between the vlincRNA located on the chromosome 3 and each gene co-expressed (either positively or negatively) with it and containing site of vlincRNA-chromatin interactions are shown by the thin lines. Box plots of the odds ratios (c), p values (d), and the total number of genes in common (e) based on the comparisons of the co-expression networks and chromatin interaction datasets for either all genes (left plots) or genes found on the same chromosome (right plots) for the 14 vlincRNA-drug combinations. f, g Top ten GO terms enriched in genes found in either negative (f) or positive (g) co-expression networks for all 407 vlincRNAs. The GO terms were ranked based on the number of vlincRNAs (X-axes) whose networks were enriched in these terms. The numbers next to each term represent % of vlincRNAs containing the term out of the total 407 vlincRNAs. h Boxplots of the Spearman correlation values of all possible pairwise combinations of mRNA-mRNA, vlincRNA-vlincRNA, and mRNA-vlincRNA