See Figure 2 figure supplement 3. (C ) Proportion of eQTMs that are positive (pos-eQTMs, yellow) or negative (neg-eQTMs, blue) overlapping vs non-overlapping (expected) distinct genomic features (promoters, CTCF binding sites, enhancers), or overlapping CpG island promoters (CGI prom) vs overlapping non-CpG island promoters (non-CGI prom).
Hence, we hypothesized that methylation sites in promoter regions from positive (pos) and negative (neg) eQTMs contribute differently (positively and negatively, respectively) to gene expression levels across genes.
aTB, tuberculosis; pos, positive; neg, negative; PPV, positive predictive value; NPV, negative predictive value.
WT CFTR organoids were used for positive (pos) and negative (neg) assay conditions.
We then correlated and utilized different properties of all datasets in order to assess: expression Quantitative Trait Loci (eQTLs), methylation QTLs (mQTLs), positive (pos) and negative (neg) expression Quantitative Trait Methylation (eQTMs).
*SAFV, Saffold virus; pos, positive; neg, negative.
HR, hazard ratio; CI, confidence interval; pos, positive; neg, negative; mut, mutated; WT, wild-type.
aMTBC, Mycobacterium tuberculosis complex; NTM, non-tuberculous mycobacteria; pos, positive; neg, negative.
*Ig, immunoglobulin; DOBV, Dobrava virus; PUUV, Puumala virus; pos, positive; neg; negative.
*IF, immunofluorescence stain; pos, positive; neg, negative; IS, induced sputum procedure; KS, Kaposi sarcoma.
