Bioinformatic analysis of RNA-seq and clinical data

The RNA-seq and clinical data of Liver Hepatocellular Carcinoma (LIHC) were downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/). The Ensembl ID was converted to gene symbol, and the expression profile was divided into lncRNA and mRNA using gencode v22 annotation. The differently expressed lncRNAs were identified by DESeq2 package, and log2FoldChange > 1 and padj < 0.001 were set as the threshold for significantly different expression. The co-expression analysis was performed using starBase database²². The Gene Ontology (GO) analysis was performed using GO database^23,24. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed using KEGG database^25–27. We also labeled tumor samples as “high” or “low” according to whether the expression of FMNL2 was higher or lower than the median value among all samples, and the Kaplan Meier plot was made by R package.