Identifying Anoikis-Related Genes in Liver Cancer

The gene expression profiles for TCGA liver hepatocellular carcinoma (LIHC), including 50 normal and 371 tumor samples, were downloaded using the R package “TCGAbiolinks”. The phenotype and survival data of the LIHC cohorts were downloaded from UCSC Xena (https://xenabrowser.net/datapages/, (accessed on 21 September 2022)). The DEGs were analyzed using the R package “TCGAbiolinks”. The p-values were adjusted based on the false discovery rate (FDR) correction method, and the DEG cutoff was set as |log₂FC| > 1 and adjusted to a p-value < 0.05.
The gene expression profiles of the GSE84402 and GSE101685 datasets, including 22 normal and 38 tumor samples, were used as validation cohorts for the prognostic model. The gene expression profiles and clinical data for the ICGC Liver Cancer-RIKEN, JP (LIRI-JP) cohorts, including 232 tumor samples, were also used as validation cohorts for the prognostic model.
A total of 794 anoikis-related genes was acquired from GeneCards (https://www.genecards.org/ (accessed on 22 September 2022)), and 448 of these genes were selected based on a score > 0.4. The overlap of DEGs for LIHC and anoikis-related genes was visualized using the R package “VennDiagram”.