2.4. Analysis of functional enrichment in immune-related lncRNAs with differential expression

The immune score information of the TCGA samples was downloaded from ESTIMATE (ESTIMATE: Disease (mdanderson.org)). Then, all samples were classified into two groups: one with high immune scores and one with low immune scores, using the median immune score as a threshold. The differentially expressed genes (DEGs) between different immune score groups, as well as those between high- and low-risk groups, were obtained using the “limma” and “edgeR” R packages. By intersecting these DEGs, 29 immune-associated differentially expressed genes (IDEGs) (Supplementary Table S3) were obtained and used for subsequent functional enrichment. Based on these IDEGs, functional enrichment analysis was performed using the “ggplot2” and “clusterProfiler” R packages. In addition, at the genomic level, gene set enrichment analysis (GSEA) has been used to evaluate biological signatures [34]. Therefore, we used the R packages “ggplot2” and “clusterProfiler” for GSEA to determine the enrichment of signaling pathways for these IDEGs.