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. 2021 Feb 5;22:47. doi: 10.1186/s12859-020-03850-6

Table 1.

Number of samples, dataset_id and URLs to download the gene expression and copy number data from UCSC Xena data server

Cancer type DataSet URLs

BRCA

(n = 1057)

 HiSeqV2_PANCAN https://xenabrowser.net/datapages/?cohort=TCGA%20Breast%20Cancer%20(BRCA)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes

LUAD

(n = 500)

 HiSeqV2_PANCAN https://xenabrowser.net/datapages/?cohort=TCGA%20Lung%20Adenocarcinoma%20(LUAD)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes

GBM

(n = 484)

 HiSeqV2_PANCAN https://xenabrowser.net/datapages/?cohort=TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes

SKCM

(n = 358)

 HiSeqV2_PANCAN https://xenabrowser.net/datapages/?cohort=TCGA%20Melanoma%20(SKCM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes