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To evaluate allelic protein-binding differences, we calculated biased allelic binding (BAB, see Methods for detail) scores for all 374 candidate SNP sites.
To determine allele-dependent enhancer activity of the 56 SNPs, we calculated biased allelic enhancer (BAE, see Methods for detail) score using allele-specific read counts and observed 20 SNPs with absolute BAE score ≥ 0.58.
The filtered BS05 × BS17 was obtained by excluding those recombinant haplotypes of BS05 × BS17 that were shared by BS05 or BS17 in the haplotype inference (see "Methods" for detail).
A risk score formula was obtained for predicting the patient survival (see materials and methods for detail).
For multiple testing corrections, we computed the false discovery rate (FDR) for each tag using statistical hypothesis testing involving Storey's method [15] (see Materials and Methods for detail).
Of these, 879 were quantified post-data normalization (Figure 2A), with the overall protein identification FDR of less than 1%% (see Materials and Methods for detail).
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See Methods and Supplementary Methods for details.
See main text and Methods for details.
(See Methods for details of the scenarios).
See Methods for details of model fitting and topologies.
See Methods for details concerning data acquisition and preprocessing.
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