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Table 2 Summary information of cis-SNPs for the 10 cancers and the association of cis-SNP effect sizes for each gene in TCGA and GTEx

From: Integrative eQTL-weighted hierarchical Cox models for SNP-set based time-to-event association studies

Cancer Mean Median Max Min R2 > 0.10 (%) FDR < 0.05 (%)
ACC 3,521 3,597 13,279 8 325 (2.9) 8533 (76.4)
BRCA 3,089 3,337 13,086 9 309 (4.0) 5265 (67.6)
COAD 3,655 3,737 12,881 4 297 (2.6) 8504 (73.7)
LIHC 3,492 3,597 8,479 3 202 (2.4) 6396 (74.6)
LUAD 3,732 3,733 12,717 20 170 (1.6) 7917 (74.6)
LUSC 3,525 3,611 12,726 6 282 (3.0) 7004 (74.2)
OV 1,935 1,750 6,752 3 977 (12.7) 5329 (69.0)
PAAD 3,801 3,784 13,382 9 167 (1.6) 7905 (73.7)
STAD 3,500 3,687 13,091 3 168 (1.8) 6496 (70.3)
UCEC 3,721 3,727 13,063 7 186 (1.7) 8086 (73.9)
Average 3,397 3,456 11,946 7 308 (3.4) 7145 (72.8)
  1. Mean: the average number of cis-SNPs across genes; Max or Min: the maximal or minimal number of cis-SNPs across genes. R2 denotes the determination coefficient of the cis-SNP effect sizes for each gene in the linear regression with the effect sizes of a gene in TCGA as response and the effect sizes of that gene in GTEx as the covariate. The last column denotes the number of genes whose regression coefficient is significant (FDR < 0.05)