FIG 7.

The strength of the canonical ISRE differentiates ISG categories. Motifs were identified in genomic sequences 500 bp upstream to 250 bp downstream of annotated transcriptional start sites (TSS) for gene sets. (A) Motif sequence logos for de novo common ISG motifs and known motifs from the HOMER database. The heights of bases are proportional to their preference at that position. The frequency graph depicts the proportion of genes in each category with at least one instance of the indicated motif scoring above the threshold, with * indicating a q value (false-discovery rate) of <0.05. (B) Histograms of motif locations relative to the TSS. (C) Comparison of ISRE (GEO series accession number GSE23622) motif scores among previously defined common, IFN-β-specific, apoptosis, and inflammatory ISGs. The dashed line indicates the threshold score from the analysis in panel A; the highest-scoring motif is shown for each gene with at least one motif score of >1. (D and E) Correlation of ISRE scores with log₂-fold changes following treatment with IFN-β (D) or IFN-λ (E). The vertical dashed line indicates the threshold score from the analysis in panel A, and the horizontal dashed line indicates a 1.5-fold differential expression cutoff.