Figure 4

Functional associations of intronic antisense lncRNAs expressed in RCC. (A) Cis-correlation analysis. Histogram of Spearman correlation values calculated using the expression levels of intronic lncRNAs and mRNAs expressed in 4303 gene loci, across RCC and three other human tissues (normal liver, prostate tumor and kidney nontumor). (B) GO enrichment analysis of the mRNAs correlated in cis with the lncRNAs from the same loci (Spearman correlation -0.5 > ρ >0.5; p <0.05; see red broken lines in panel A). Color scale indicates increasingly higher statistical significance of enriched GO terms: Yellow, p = 0.05; Dark orange, p <0.0001. (C) Trans-correlation analysis. Module map of lncRNAs and GO enriched terms among trans-correlated mRNAs. Analysis was performed with the 20% most abundant lncRNAs (columns) that showed Spearman correlation values in the ranges -0.7 ≥ ρ ≥0.7 between its expression level in RCC and in three other human tissues (normal liver, prostate tumor and kidney nontumor) and the expression of mRNAs outside the host locus (correlation in trans; p <0.05); GO terms significantly enriched among trans-correlated mRNAs are shown in the rows (p <0.05 with Bonferroni correction). Colors indicate if the majority of the mRNAs within that GO is directly (yellow) or inversely (blue) correlated with the lncRNA. A black entry indicates no significant enrichment. The lists of GO enriched terms and of mRNAs belonging to each term for panels 4B and 4C are given in Additional file 10: Table S7.