Fig. 4: Functional annotation of lncRNA promoters.

a Schematic overview of the definition of lncRNA promoters not overlapping with a protein coding gene locus. bp: base pair; PC: protein-coding; TSS: transcription start site. b, c Average normalized counts for ATAC-seq peaks mapped to lncRNA promoters in estrogen receptor (ER) positive (+) (blue dots) (n = 58) and ER negative (−) (red dots) (n = 12) breast tumor samples from the TCGA-BRCA cohort. Wilcoxon test p-values are denoted. The line within each box represents the median. Upper and lower edges of each box represent 75th and 25th percentile, respectively. The whiskers represent the lowest datum still within [1.5 × (75th −  25th percentile)] of the lower quartile, and the highest datum still within [1.5 × (75th  −  25th percentile)] of the upper quartile. b Promoters of independent lncRNAs overexpressed in ER positive cases and c promoters of independent lncRNAs overexpressed in ER negative cases. d, e Enrichment of independent lncRNA promoters across ChromHMM genome segmentation from breast cancer cell lines. Enrichment is calculated as the ratio between the frequency of lncRNA promoters found within a specific segment type, over the frequency of all lncRNA promoters within the same segment type. The length of the bars (x-axis) shows the log transformed BH corrected p-value from the hypergeometric test. d Promoters of independent lncRNAs overexpressed in ER positive cases and e promoters of independent lncRNAs overexpressed in ER negative cases. Active Enhancer=EhAct, Active Promoter = PrAct, Repeat Zink Finger = RpZNF, Flanking Promoter region = PrFlk. f, g Swarm plots showing enrichment of TF binding sites (–(log10(p-value) using Fisher’s exact tests) on the y-axis for specific sets of promoters according to UniBind. TF names of the top 10 enriched TF binding sites data sets are annotated by colours. f Promoters of independent lncRNA overexpressed in ER positive cases and g promoters of independent lncRNAs overexpressed in ER negative cases.