Identification of Prognosis-Related eRNA in GBM

PreSTIGE, an algorithm that could predict tissue-specific enhancers based on the H3K4me1 mark and tissue-specific expression of mRNAs, was applied to predict lncRNAs expressed from active tissue-specific enhancers and their target genes (Corradin et al., 2014; Vucicevic et al., 2015). Ensembl transcript ID and gene symbol were annotated by “biomaRt” R package (human GRCh38.p13) (Durinck et al., 2009; Smedley et al., 2009). The log-rank test was used to calculate the differences between eRNA expression (cutoff value = 50%) and survival time in GBM patients using a threshold of p < 0.05. Based on the result of log-rank test, Kaplan–Meier curves were plotted to indicate the survival time differences. According to the list of eRNAs and target genes, Spearman correlation test was used to evaluate correlations and Spearman rank correlation coefficient r > 0.4, p < 0.001 as the threshold.