Table 1

Comparison of iASeq and AlleleSeq
Gold standard ChrX All Caltech ASE exonic SNPs Autosomal Caltech ASE exonic SNPs
TF Td AlleleSeq iASeq Td AlleleSeq iASeq Td AlleleSeq iASeq
YaleCFOS 41 3 4 9 5 3 9 5 3
YaleMYC 122 9 22 39 5 10 38 5 10
YaleJUND 289 13 31 24 4 8 23 4 7
YaleMAX 105 3 18 18 3 1 18 3 2
YalePolIII 25 2 2 0 0 0 0 0 0

Column 1: TF name. Column 2: Tdis the number of AlleleSeq reported ASB SNPs. Columns 3-4: the number of non-pseudoautosomal region X chromosome SNPs among the top Tdallele-specific SNPs reported by AlleleSeq and iASeq. Column 5: Tdis the number of AlleleSeq reported ASB SNPs that had an exonic SNP within their 10kb neighborhood. Columns 6-7 show among the top Tdallele-specific SNPs reported by AlleleSeq and iASeq, how many SNPs had ≥1 exonic ASE SNP in their 10kb neighborhood according to the Caltech RNA-seq experiment. Column 8: Tdis the number of AlleleSeq reported autosomal ASB SNPs that had an exonic SNP within their 10kb neighborhood. Columns 9-10 show among the top Tdautosomal allele-specific SNPs reported by AlleleSeq and iASeq, how many SNPs had ≥1 exonic ASE SNP in their 10kb neighborhood according to the Caltech RNA-seq experiment. Additional file 7: Table S3 contains similar results using Yale RNA-seq exonic ASE SNPs as gold standard.

Wei et al.

Wei et al. BMC Genomics 2012 13:681   doi:10.1186/1471-2164-13-681

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