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. 2020 Feb 29;48(6):2866–2879. doi: 10.1093/nar/gkaa123

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© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Unthresholded approach for detecting TF binding affinity CRM variant associations with gene expression and their validation using GUESSFM. (A) Example of a CRM with multiple SNPs affecting the affinity for the same TF, SIN3A. (B) Association between log-fold change in CRM affinity for SIN3A (relative to the highest affinity allele observed in GM12878) and mRNA level (normalized PEER residuals) of the connected gene, SLC29A3 (gene-level FDR adjusted P-value = 1.60 × 10⁻⁴, β = −0.14). (C, D) Examples of loci, whereby the SNP predicted to have the strongest impact on a CRM’s binding affinity for a given TF has been fine-mapped as a potentially causal variant driving the locus’s association with the expression of a physically connected target gene (GUESSFM ). (C) eGene: MB21D2; eQTL rs2886870, predicted to affect NFKB binding affinity. (D) eGene: PIEZO2; eQTL rs12455452, predicted to affect TCF12 binding affinity. See insets for the effects of the SNPs on the respective TF's PWM match.

Inline graphic — Unthresholded approach for detecting TF binding affinity CRM variant associations with gene expression and their validation using GUESSFM. (A) Example of a CRM with multiple SNPs affecting the affinity for the same TF, SIN3A. (B) Association between log-fold change in CRM affinity for SIN3A (relative to the highest affinity allele observed in GM12878) and mRNA level (normalized PEER residuals) of the connected gene, SLC29A3 (gene-level FDR adjusted P-value = 1.60 × 10⁻⁴, β = −0.14). (C, D) Examples of loci, whereby the SNP predicted to have the strongest impact on a CRM’s binding affinity for a given TF has been fine-mapped as a potentially causal variant driving the locus’s association with the expression of a physically connected target gene (GUESSFM ). (C) eGene: MB21D2; eQTL rs2886870, predicted to affect NFKB binding affinity. (D) eGene: PIEZO2; eQTL rs12455452, predicted to affect TCF12 binding affinity. See insets for the effects of the SNPs on the respective TF's PWM match.