Fig. 4: Massively parallel reporter assay for the characterization of 3′-UTR immune-related cis-eQTLs. | Nature Communications

Fig. 4: Massively parallel reporter assay for the characterization of 3′-UTR immune-related cis-eQTLs.

From: Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci

Fig. 4

A Protocol followed for 3′-UTR MPRA assay. Ref: Reference allele, Alt. allele: Alternative allele, Syn. pA terminator: synthetic polyadenylation terminator, oligodT: primer containing 20 T nucleotides. Created with Biorender.com. B Manhattan plot showing the top hits from the MPRA assay in both gastric cancer cell lines. A two-sided Wilcoxon rank sum test was used to calculate p value of enrichment of alternative vs reference alleles and multiple comparison adjustment was performed by FDR. The black line (p. adj. = 0.05) separates significant from non-significant calls. Blue dots represent likely germline variants, while red dots represent likely somatic variants. Figure data are provided in the Source Data file.

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