Fig. 4.

Physically Interacting genes are co-expressed. (A) Schematics of the complete PPI and NCI network. A noncoding RNA “X” interacts with three proteins “A”, “B” and “C”, and protein “B” binds to protein “D”. (B) The PPI network contain only interactions among proteins, and all interactions containing NC interactions are absent. (C) The induced NCI (iNCI) contains indirect interactions. ncRNA “X” interacts with genes “A” and “B”; therefore, they are co-regulated by the same ncRNA, leading to an indirect interaction. In the same fashion, proteins “A” and “C” and “B” and “C” are also co-regulated by the same ncRNA “X”, inducing a triangle among them. (D) PPI & iNCI includes direct and indirect interactions. Combining the interactions identified in (B and C). (E) Genes with direct or indirect physical binding (PPI, PPI & NCI, or co-regulated by an ncRNA) have higher co-expression values than genes that do not physically interact. The boxplot indicates that the absolute Pearson correlation is higher when there is physical interaction, compared to then nonexisting links, indicating an association between physical binding and strength of co-expression. (F) Co-expression networks can predict physical interactions. We use the correlation values between two transcripts to predict a direct or indirect binding, finding that the inclusion of ncRNAs increases the AUC in the iNCI and the PPI & iNCI.