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[Preprint]. 2023 Nov 29:2023.08.15.553416. Originally published 2023 Aug 17. [Version 3] doi: 10.1101/2023.08.15.553416

Figure 3. L1 trans-eQTLs are associated with subtle, widespread differences in TE families and known TE-associated pathways.

Figure 3.

(A) Scheme for functionally annotating gene-linked index SNVs by GSEA. (B) GSEA analysis for shared, significantly regulated TE family gene sets across genotypes for rs11635336 (IL16/STARD5), rs9271894 (HLA), and rs1061810 (HSD17B12). (C) GSEA plots for the L1 family gene set results summarized in (B). For these plots, the FDR value is listed. (D) GSEA analysis for shared, significantly regulated, evolutionary-age-stratified L1 gene sets across genotypes for rs11635336 (IL16/STARD5), rs9271894 (HLA), and rs1061810 (HSD17B12). L1M subfamilies are the oldest, L1P subfamilies are intermediate, and L1PA subfamilies are the youngest. GSEA analysis for top, shared, concomitantly regulated (E) MSigDB Hallmark pathway, (F) GO Biological Process, and (G) Reactome pathway gene sets across genotypes for rs11635336 (IL16/STARD5), rs9271894 (HLA), and rs1061810 (HSD17B12). Shared gene sets were ranked by combining p-values from each individual SNV analysis using Fisher’s method. In each bubble plot, the size of the dot represents the −log10(FDR) and the color reflects the normalized enrichment score. FDR: False Discovery Rate.