Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology (original) (raw)
Figure 3
Candidate RA and CD genes are preferentially expressed in immune tissues.
We obtained tissue expression data for 126 different cell types from a publicly available database, which was grouped into immune, gastrointestinal (GI), neuronal and ‘other’ [46]. For each tissue, we compared the expression of RA (A) and CD (B) candidate genes to the rest of the genes in the genome using a one-tailed rank-sum test, resulting in a p-value for each tissue (-log(p) is plotted on the y-axis). A significant difference for a given tissue indicated that the candidate genes were enriched for expression in that tissue compared to all genes in the genome. To test whether our network prioritization identified genes that were co-enriched in specific tissues beyond what was expected from all genes in associated regions, we calculated the same p-values for the rest of the genes in RA and CD associated loci (i.e., the genes that weren't prioritized via our network permutations). In this figure, we plot the tissue enrichment scores for each tissue for the candidate genes (purple) and the non-prioritized genes in the remaining regions of association (black). We indicate the category of tissue on the bottom: immune (red), GI (yellow), neuronal (green) and other (blue). We ordered the tissues by decreasing enrichment score of the candidate genes.