Figure 2: Enrichment of the breast cancer AVS in FGFR2-related gene loci.
From: Master regulators of FGFR2 signalling and breast cancer risk
(a) VSE plots for the breast cancer AVS and the FOXA1 and ESR1 cistromes in E2-treated MCF-7 cells. (b) E2- and FGFR2-responsive genes in MCF-7 cells are tested for functional association with risk AVS by cis-eQTL analysis using METABRIC tumour gene expression data. (c–e) The same genes tested for functional association with other cancer risk AVS by cis-eQTL: (c) the prostate cancer AVS, (d) the colorectal cancer AVS and (e) the bone mineal density AVS. Box plots in each panel show the normalized null distributions (box: 1st–3rd quartiles; bars: extremes). Black diamonds show the corresponding VSE scores. Red diamonds highlight mapping tallies that satisfy a Bonferroni-corrected threshold for significance (P<1e-4). P-values are based on null distributions from 1,000 MRVSs. Binary matrices show clusters of risk-associated and linked SNPs with at least one SNP mapping to the genomic annotations and validated by cis-eQTL analysis. The bottom row of numbers indicates the number of linked SNPs in each SNP cluster. The mapping tally shows the number of clusters per annotation. Rows highlighted in dark grey show statistically significant enrichment. The cis-eQTL analysis extends the original VSE method by conditioning the mapping tallies to functional links. Non-disjoint AVSs with risk-associated SNPs in LD were merged in order to avoid inflated mapping tallies.
