Gene Expression Data Acquisition and Bioinformatics Analysis

Gene Expression Profiling Interactive Analysis (GEPIA)-(http://gepia.cancer-pku.cn/) (25) is an online server for the profiling and interactive analyses of gene expression in cancer and normal samples. Oncomine (https://www.oncomine.org/) (26, 27) is an online cancer microarray database and integrated data-mining platform. We searched PC in the two databases to analyze PC expression in THCA and other types of cancer. In addition, we used expression profiling arrays (GSE60542) from Gene Expression Omnibus databases to analyze the differentially expressed genes between THCA tissues from patients with or without lymph metastasis. The GSE60542 dataset was analyzed by the Affymetrix Human Genome Array with the annotation platform GPL570 [HG-U133_plus_2]. The GSE60542 dataset contained 14 PTC samples from patients with no lymph node metastasis, 19 samples from patients with lymph node invasion and 10 control samples from patients with normal thyroids. Using R packages, we assessed the raw GSE60542 dataset by background correction, normalization, expression calculation, and probe integration. Robust multiarray averages (RMAs) and mismatch probes (PMs) were created for processing the datasets. P-values were adjusted by the Benjamini–Hochberg method, and fold changes (FC) were calculated using the false discovery rate (FDR) procedure. Differentially expressed genes (DEGs) with a |log2-fold change| >1 and P <0.05 in PTC samples versus normal samples were selected. The basic features from the Gene Expression Omnibus (GEO) database are shown in Table 1 .

Basic features of the GSE 60542 database.