Fig. 2

Breast cancer ICR-associated lncRNAs and associated biological pathways and functions. A Volcano plot of differentially expressed lncRNAs in ICR high vs low breast tumors from the TCGA breast cancer cohort. red = log2 fold change > 1 and adj p-value < 0.05, blue = adj p-value < 0.05, and green = adj p-value > 0.05. B Representation of the number of differentially expressed lncRNAs by ICR in TCGA-BRCA and their proximal protein-coding genes as per the RWR propagation algorithm. Protein coding genes with confirmed up- or downregulation as per differential expression analysis of RNAseq data are indicated with asterisks. The mRNA expression of 59 up- and 68 downregulated genes was available in the RNAseq data, and the differential expression of 37 and 40 genes was confirmed. C Pathway enrichment analysis of proxy protein-coding genes using ConsensusPathDB. For each pathway, the number of differentially expressed genes is indicated and the proportion of up- and down regulated genes in ICR high vs ICR low is visualized in red and green respectively. D IPA analysis of diseases and functions associated with top-ranked proxy protein-coding genes