Fig. 4

LncRNA:DNA triplex-forming sites as predictors for TADs. (A) Triplex-forming sites (TFSs) in n TADs and in the background set consisting of n randomly selected genomic regions, which do not overlap with TADs. (B) The frequency of TFSs for lncRNAs is used as features in a prediction problem, where TADs and the random regions have class labels “1” and “0”, respectively. (C) The predictive models are trained on the training set (80 % of 2n) to determine the appropriate model parameters. The model performances are computed on the test data (20 % of 2n). (D) Prediction accuracies and four other metrics of the predictive models. The values are averaged across the six cell lines (E) TAD-lncRNA DANCR with its triplex-forming domain (TFD) located from base pair position 679 to 702. (F) Genomic annotation of locations of the TFSs of DANCR in GM12878 cell line. (G) Top gene ontology terms associated with the genes nearest to the TFSs of TAD-lncRNA DANCR in the GM12878 cell line. X-axis indicates -log10 p-value