Data processing of acquisition and identification of differentially expressed genes (DEGs)

Microarray data for ICC were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Two expression profiling datasets, {"type":"entrez-geo","attrs":{"text":"GSE26566","term_id":"26566"}}GSE26566(27) and {"type":"entrez-geo","attrs":{"text":"GSE107943","term_id":"107943"}}GSE107943(28), were obtained. The {"type":"entrez-geo","attrs":{"text":"GSE26566","term_id":"26566"}}GSE26566 dataset contained 104 ICC samples and 6 normal samples. The {"type":"entrez-geo","attrs":{"text":"GSE107943","term_id":"107943"}}GSE107943 dataset contained 30 ICC samples and 27 normal samples, as well as clinicopathological information regarding the tumor samples. All expression profiles were downloaded and processed using the R package of GEOquery (29). The transcriptome profiles of 32 ICC samples and 9 normal samples and clinical information of tumor samples were obtained from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/) and analyzed using the R package of TCGAbiolinks (30). The {"type":"entrez-geo","attrs":{"text":"GSE26566","term_id":"26566"}}GSE26566 and TCGA datasets were analyzed separately as volcano maps using GraphPad Prism 9 (GraphPad Software; Dotmatics). Log₂ fold-change (FC)>1 and P<0.05 were defined as the screening thresholds. Common DEGs of the {"type":"entrez-geo","attrs":{"text":"GSE26566","term_id":"26566"}}GSE26566 and TCGA datasets were obtained through the TBtools (31). For the definition of high or low expression levels of ITGB5 in the {"type":"entrez-geo","attrs":{"text":"GSE107943","term_id":"107943"}}GSE107943 and TCGA datasets, the expression of ITGB5 was divided into two groups according to the survival status of patients with ICC, and separate receiver operating characteristic curves were obtained to determine the ITGB5 cut-off value with area under the curve >0.8 and P<0.05.