TCGA Data Download and Preprocessing

Gene expression quantification data and corresponding clinical information for HCC were downloaded from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data collection. The 424 HTSeq-counts files comprised 371 tumor samples and 50 normal samples. Clinical information was extracted and included follow-up time and clinical status. The TCGA expression matrix was obtained by data fusion and ID transformation of raw TCGA counts data. Next, the RPKM (Reads Per Kilobase per Million mapped reads) values were calculated for the WGCNA.

We applied the “limma” package (Ritchie et al., 2015) of R software to perform normalization and base-2 logarithm conversion for the matrix data for each GEO and TCGA dataset. differentially expressed genes for each GEO and TCGA matrix were obtained by transforming expression values, and genes were sorted according to the log₂FoldChange (logFC) value. Next, rank analysis was performed using the R package “RRA.” The criterion for screening DEGs is that the P < 0.05 and | logFC | > 1.