Varsan2 somatic mutation data of 487 PTC patients was download by R package “TCGAbiolinks”16. The counts data of RNA high throughput sequencing (HTSeq-counts) of 502 PTC patients, including 58 normal tissues and 502 tumor tissues, was downloaded by R package “GDCRNAtools” from TCGA17. The low-expression gene was defined as the gene with the value of count-per-million (CPM) < 2 in more than half of the samples. After filtering out low expression genes, 13483 protein-coding genes (messenger RNA, mRNA) were extracted by transformed with GENCODE (https://www.gencodegenes.org/). Clinical information of the 502 patients was downloaded from UCSC Xena by R package “UCSCXenaTools”18. By intersecting 502 PTC patients with expression data and 487 PTC patients with mutation data, 482 cases meeting the following criteria were included in our analysis: Patients with clear BRAF mutation information; Patients with gene expression data of RNA-sequencing. Raw data of 108 PTC samples with specific BRAF mutation status were collected from three microarray datasets (accession numbers: GSE27155, GSE54958, and GSE58545) in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The expression data were processed as the previous description11.

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