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Fig. 2 | Genome Biology

Fig. 2

From: Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci

Fig. 2

pcRNA expression and regulation. a Density distribution of the Spearman’s correlation coefficients between pcRNAs and corresponding coding genes in human tissues and cell lines (mean Spearman’s rho 0.25, permutation test p value < 10−6). The dotted line shows the background distribution of all pairwise Spearman’s correlations between pcRNAs and pcRNA-associated coding genes. Inset: Distributions of the Spearman’s correlation coefficients divided by the positional category of the pcRNA. AS antisense, BT bidirectional, DS-AS downstream antisense, DS-S downstream sense, OLAP overlapping, US-AS upstream antisense, US-S upstream sense. b Nanostring expression profiles of FOXA2 and FOXA-DS-S across human (top) and mouse (bottom) tissues. The points indicate the mean value of two technical replicates, while the vertical bars report the value of each replicate. c Transcription factor binding patterns in the promoters of pcRNAs (middle), their associated coding genes (left), and across pcRNA loci (right). The heatmaps present the distribution of experimentally validated TF-binding sites from 2216 ENCODE ChIP-Seq experiments (y-axis), showing a high degree of co-occupancy between the promoters of pcRNAs (x-axis) and their associated coding genes. The blue bar graph on top of each heatmap shows correlation (r values) between a pcRNA and its associate coding gene. The color bars next to the right heatmap indicate the TF groups showing dominant binding patterns. d Same as in c but indicating the presence of TF-binding motifs based on known motifs annotated in JASPAR (freeze 2014–12–10, 263 motifs), in Kheradpour and Kellis [100] (2065 motifs) and in Jolma et al. [101] (843 motifs)

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