Certain histone marks and TFs are enriched in lincRNA promoters. (A) Fisher effect size differences, comparing the presence or absence of eight histone marks (observed via ChIP) in the promoters of lincRNAs and mRNAs, in seven ENCODE cell lines. Blue corresponds to larger values in mRNAs and red to larger values in lincRNAs. The number of genes ranged from 754 (HUVEC) to 1262 (GM12878) and corresponds to all lincRNAs expressed at >0.1 FPKM in the tested cell line, and to expression-matched mRNAs. (B) ChIP-seq read coverage for three histone marks in one lincRNA (left) and one mRNA (right) with similar expression levels in H1 ESCs. (C) Wilcoxon effect size differences between lincRNAs and mRNAs across several gene/promoter properties. The genes analyzed are the same as in A. (D) Fisher effect size differences between lincRNA and mRNA promoters comparing the presence or absence of TFs, in HUVEC cells. (E) Average conservation at FOS (left) and GATA2 (right) binding sites overlapping lincRNA and mRNA promoters centered on ChIP-seq peaks. Width of the lines represents the standard error. (F) Histogram of the number of lincRNAs with different numbers of TFs with conserved binding sites in their promoters (bars, left axis) and the corresponding median expression for that group of lincRNAs (dots, right axis). The identity of notable functional lincRNAs within each group is highlighted.