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Table 2 Number of SNPs (and genes) tested and number of significant associations (p < 0.0001) in ASE, PO-ASE and eQTL analyses

From: Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Analysis Definition Angus Holstein Meta-analysis
Muscle Liver Liver WBC
ASE No. tests 3,749,255 (3022) 3,766,137 (2903) 8,639,073 (5803) 11,419,065 (6873) 20,248,509 (9155)
No. Sig 11,717 (261) 8250 (79) 5926 (149) 11,299 (194) 1,528,756 (7357)
FDR 3% 5% 15% 10% 0.1%
PO-ASE No. Sig. 6748 (67) 594 (18) 1048 (56) 1739 (69) 1,199,496 (6255)
FDR 6% 63% 82% 66% 0.2%
eQTL No. tests 8,364,720 (12,278) 7,326,437 (12,233) 9,866,261 (14,373) 9,641,386 (14,175) 13,373,638 (16,038)
No. Sig. 45,310 (1796) 32,230 (850) 27,107 (579) 22,974 (620) 151,636 (4051)
FDR 2% 2% 4% 4% 1%
Meta-analysis No. tests 10,855,138 (12,283) 9,955,525 (12,240) 15,886,606 (14,379) 17,836,290 (14,179) 28,807,218 (16,043)
No. Sig. 78,539 (1997) 75,667 (950) 84,135 (776) 63,589 (855) 1,377,335 (8317)
FDR 1% 1% 2% 3% 0.2%
  1. The number of dSNP-tSNP pairs tested and significant (p < 0.0001) in ASE and PO-ASE analyses and the number of gene-SNP combinations tested and significant (p < 0.0001) in local eQTL mapping are shown in the table. The number SNPs tested or significant in the analyses are associated with fewer numbers of genes which are shown in parenthesis. Generally, combining the results in meta-analyses within and across RNA-Seq datasets reduce the FDRs