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Fig. 3 | Genome Biology

Fig. 3

From: cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Fig. 3

local-eQTL analysis links natural variation to gene expression levels. a Infection leads to the differential expression of around 2400 genes (BH-corrected p value < 0.05, fold change > 2). b Metaplot of the location of local-eQTLs with respect to their associated genes’ transcription start sites (TSS). The gray, blue, and orange lines represent the control, shared, and infected conditions respectively. Since SNP density is not uniform in the genic windows, the black lines represent the density of random samples of SNPs drawn from the pool of all SNPs that were included in the local-eQTL scan. Specifically, they are 100 samples of 5904 SNPs, which is equal to the number of detected local-eQTLs in the infected condition. c Graphical representation of enriched biological process gene ontology terms based on the lists of genes with significant cis-eQTL associations. The GO analysis was performed using the GOstats [50] R package (hypergeometric test p value < 0.005), and REVIGO [51] was used to reduce redundancy in the ontology groups and plot them by semantic similarity (allowed similarity = 0.7). The size of the circle indicates the number of genes belonging to a certain GO category, and the color indicates enrichment significance. The log10(p value) is the hypergeometric test FDR-corrected p value enrichment result. The X/Y space is the multidimensional scaling (MDS) of the pairwise semantic similarity measures (simRel). Closer terms in this 2D space imply closer GO terms (based on their similarity). d Differential enrichment of TF motifs around condition-specific local-eQTLs. Separate analyses were performed on i-cisTarget using regions of 201 bp centered around local-eQTLs specific to the control or infected condition. The difference between the infected and control normalized enrichment scores (NES) from the two analyses was calculated for each tested motif/feature. The color of the motif indicates the source database [52, 53]. The top 15 motifs from each side as well as the 15 motifs closest to 0 are labeled

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