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Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

Figure 1

Uniform analysis of multi-cell type eQTL data sets.

Studies are labeled by their acronym from Table 1. (A) Plot of (y-axis) as a function of (x-axis), for each study as a separate line of a diferent color, as indicated in panels B, D, and E. Dashed line represents . (B) Plot of eQTL counts as function of , for all studies. (C) eQTL count (x-axis) by tier, for tiers 1–4 (light blue, dark blue, light green, and dark green, respectively), with separate bars for each study (y-axis). (D) Fraction of genes with a significant eQTL SNP (y-axis; thresholded at ), as function of sample size (x-axis). Each study is plotted in a distinct color, as indicated with labels. Studies with replicate expression measurements are depicted as triangles, studies without as circles. (E) Fraction of genes with a significant eQTL that have more than one independently associated SNP (y-axis; thresholded at ), as a function of sample size (x-axis). Each study is plotted in a distinct color. Studies with replicate expression measurements are depicted as triangles, studies without as circles. (F) Histogram of eQTL counts by tier (y-axis; colors as in panel C), summed across studies, as a function of their distance to the gene transcription start and end sites (x-axis; gene split into 10 bins). P (grey) line depicts the counts of first tier eQTL SNPs from a permutation, to illustrate the background distribution of tested SNPs.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1003649.g001