Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses
(A) For each nonhuman species, ISGs with one-to-one orthologs that were up-regulated in the human interferome and an identical number of random genes not differentially expressed by IFN stimulation were selected. dN and dS values were then retrieved from the Ensembl database. Histograms show dN/dS ratio values for ISGs (blue) and non-ISGs (red). Differences in the distribution of dN/dS values of the non-ISGs compared to ISGs were tested using the Kruskal–Wallis rank sum test and Wilcoxon rank sum test with continuity correction. (B) The extent of gene expansion was compared between ISGs and the genome as a whole. The y-axis represents the ratio between the number of genes for which there are paralogs (multiple) and those which are orthologs (single) as a proxy for gene expansion. Boxes and whiskers represent the values for 500 randomly selected non-ISGs, while ‘×’ represents the mean value for the ISGs for each species. With the exception of the sheep, all ISG values were above the median value. The code used for the random sampling and the generation of Fig 4A and 4B is provided in S3 Data and S4 Data, respectively, with the input file available as S5 Data. (C) Up- or down-regulated genes were divided into bins according to the number of species in which they were differentially expressed. The extent of gene expansion was calculated as panel B (S1 Data). A positive trend was identified for up-regulated genes whereby the greater the number of species which up-regulate a gene, the greater the likelihood of copies being retained (P < 0.05). IFN, interferon; ISGs, interferon-stimulated genes; K-W, Kruskal-Wallis; W, Wilcoxon rank sum test.