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A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells

Figure 5

The ASE ratio alone reveals tissue- and person-specificity of regulatory differences.

Of the 695 heterozygous expression SNPs commonly shared between PGP1 and PGP9, we selected 186 expression SNPs that were detectable in 17 out of 17 cDNA samples (three samples with a very low sequencing depth were excluded). Using log2-transformed ASE ratios derived directly from the sequencing counts, we performed hierarchical clustering of samples and expression SNPs (green: reference allele; red: alternative allele). We identified highly individual-specific clusters from the ASE ratio alone in the absence of any genotyping data. In addition, most tissue-specificity relationships were determined correctly from the ASE ratio.

Figure 5

doi: https://doi.org/10.1371/journal.pgen.1000718.g005