Screening for differentially expressed genes (DEGs)

The raw data of the gene expression profiles were analyzed using R software v3.5.2 (https://www.r-project.org) and the Bioconductor package ‘Limma’ v3.36.5 (https://bioconductor.org/packages/limma/) (18). The robust multi-array average method (19) was used to complete background correction and normalization of all original microarray data. Subsequently, the present study used the combat function of the ‘sva’ package v3.30.1 (https://bioconductor.org/packages/sva/) (20) of R to remove any batch effect. DEGs were screened using the ‘Limma’ package, and the Bioconductor package ‘edgeR’ v3.24.3 (21) was used to analyze and process the data downloaded from TCGA database. The screening criteria for DEGs were both adjusted to P<0.01 and |log fold-change| >2.0.