Figure 4: Relationships between lineage-specific lncRNAs and co-expressed protein-coding genes.

(a) Results are expressed as the % of protein-coding genes co-expressed with lineage-specific lncRNAs relative to total genes within the indicated distance from the lineage-specific lncRNA as a function of distance from the lncRNA in kilobases. (b) As in a except results are expressed relative to the number of genes in the genome away from the lineage-specific lncRNA. (c) Percentage of co-expressed genes transcribed in the antisense or sense orientation relative to the adjacent lncRNA. (d) Percentage of lncRNA-protein-coding gene lineage-specific clusters containing the indicated numbers of co-expressed protein-coding genes. See also Supplementary Table 1. (e) Genes encoding lineage-specific mRNAs are enriched in the genome within lineage-specific lncRNA gene clusters. The y axis is the percent of total lineage-specific (TH1, TH2 and TH17) mRNAs defined as threefold overexpressed in TH1, TH2 or TH17 cultures relative to the other two lineages. The x axis is the distance of the gene encoding a TH1-, TH2- or TH17-specific mRNA from the nearest gene encoding a TH1-, TH2- or TH17-specific lncRNA. P values determined by χ² analysis.