Differentially expressed lncRNAs

The expression levels of extracted 9511 lncRNAs were scale to the z-score across all the genes according to the following equation first:

where μ is the mean of expression levels of each lncRNA and σ is the standard deviation. Using the scaled expression levels, R package limma [14] was used to identity the differentially expressed genes between the control group and the patients. Moderated t-statistics is used to for significance analysis where the standard errors were moderated across genes using the Bayesian model [15]. This step borrowed information from the collection of genes to help with inference about every individual gene.

For the differentially expressed lncRNAs, we also used COXPH to study whether their expression levels were associated with the prognosis.