ISG15 and infection: Gene ontology analysis of ubiquitin sites gained and lost following infection (clusters 3 and 4, respectively) revealed that certain substrates are similarly enriched among ubiquitin targets and ISG15 sites (nucleotide binding and cellular metabolic processes), however, others inversely correlated with ISG15 sites (cofactor binding, coenzyme binding, lyase and ligase activity, Fig. 3d).