Extended Data Fig. 1: Genomic features of co-localized Triplex Target hotspot.
From: Three-dimensional genome organization via triplex-forming RNAs
(a) Percentage of TrTS that co-localize genome-wide versus the length of the identified lncRNAs with triplex forming potential. The blue line represents a linear regression model fit and the transparent shade is the 95% confidence interval. (b) Top three enriched motifs (Methods) for co-localizing Triplex Target Sites over background obtained with HOMER99. (c) Enrichment of co-TrTS hotspots in DNase I hypersensitive sites. (d) Number of lncRNAs with triplex forming potential with respect to chromosomal gene density. (e) Co-TrTS potential distribution per-chromosome for the four clusters defined in Fig. 2e. Box boundaries represent 1st and 3rd quartiles, middle line represents median, and whiskers extend to 1.5 times the interquartile range (two-sided Mann-Whitney rank test, using python default parameters, ***: p < 10−3; n = 897, 506, 667, and 575 for cluster 1, 2, 3, and 4, respectively. (f) Compartmentalization saddle plot (Methods) of all intra-chromosomal interactions in GM12878 cell line.
