Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses
(A) Sinaplot showing the differential expression values (log2FC) of 40 genes previously published as exerting antiviral activity (red dots) (S2 Table) as opposed to the rest of the ISGs (grey dots). ISGs (including antiviral ISGs) were allocated to bins according to the number of species in which they were found to be up- or down-regulated (i.e., the corevert ISGs are bin 10). The majority of antiviral ISGs (red) were found to be up-regulated in at least eight species (S1 Data). (B) Graph showing the extent of up-regulation of antiviral ISGs compared to nonantiviral ISGs. The mean log2FC of 40 known antiviral ISGs (indicated with an asterisk on the plot) is compared to 100 samplings of 40 randomly selected ISGs from the interferome of each species (box and whiskers). In all cases, antiviral ISGs are up-regulated to a significantly greater extent as compared to nonantiviral ISGs (P < 0.01 for each species). The code used for random sampling and the generation of Fig 3B is available in S2 Data, with the required input files available as S5 Data and S6 Data. (C) Boxplots showing basal transcription levels (expressed as FPKM) and differential expression (log2FC) in response to IFN of known antiviral ISGs as in panels A and B. Every ortholog for each gene is indicated with a dot coloured according to species. The median FPKM value for the entire interferome is indicated with a broken line (S1 Data). FPKM, fragments per kilobase mapped values; IFN, interferon; ISGs, interferon-stimulated genes; log2FC, log2 fold change.