Figure 2.

Enrichment of the lncRNA hybridization targets predicted by ASSA among differentially expressed genes identified in the FANTOM6 ASO knockdown experiments in two modes. (A,B) ASSA was applied to the differentially expressed and background transcripts assuming co-transcriptional or post-transcriptional lncRNA:RNA interaction mode. The-${log}_{10}$ of enrichment p-values were computed using the hypergeometric (HGD) and GSEA tests. Knockdowns with either p-value $<0.01$ are marked by the red color. There were 98 and 47 such ASOs for the co- and post-transcriptional modes, respectively. (C) The majority (41 out of the 47) of the ASOs with significant p-values in the post-transcriptional mode also had significant p-values in the co-transcriptional mode. (D) The heatmap showing four p-values for the 41 ASOs that produced strong p-values in both the co- and the post-transcriptional modes. The 41 ASO ids are on the right side and the corresponding 31 lncRNA gene names are on the left side of the heatmap. The p-values of the co-occurrence with the iMARGI peaks are shown on the right.