function Enrichment Score Enrichment p- value % genes in group that are present # genes in list, in group type I interferon-mediated signaling pathway E cytokine-mediated signaling pathway E response to virus E immune response E innate immune response E interferon-gamma-mediated signaling pathway E double-stranded RNA binding E chemotaxis E-0611 negative regulation of type I interferon production E defense response to virus E inflammatory response E ISG15-protein conjugation E phagocytosis, engulfment E blood circulation E negative regulation of viral genome replication E response to biotic stimulus positive regulation of interferon-alpha production nucleosome IgG binding cellular copper ion homeostasis superoxide-generating NADPH oxidase activity cell-cell signaling cellular response to heat copper ion transport nucleosome assembly ISG15 ligase activity regulation of defense response to virus intracellular transport of viral proteins in host cell cellular response to interferon-alpha interleukin-1 beta secretion detection of virus RNA catabolic process cytosol modification-dependent protein catabolic process negative regulation of defense response to virus by host pathogen-associated molecular pattern dependent induction by symbiont of host innate immunity tryptophan catabolic process to kynurenine protein kinase inhibitor activity microglial cell activation involved in immune response response to lipopolysaccharide negative regulation of erythrocyte differentiation tryptophan catabolic process hydrolase activity, acting on acid anhydrides positive regulation of immune response chemokine activity response to cold positive regulation of tumor necrosis factor biosynthetic process JAK-STAT cascade protein dimerization activity defense response to bacterium Table S2. GO categories upregulated in early acute phase vs convalescent phase(P < 0.05) (HG-focus platform)

cyclin-dependent protein kinase inhibitor activity soluble fraction activation of pro-apoptotic gene products positive regulation of interferon-beta production phosphatidylinositol binding complement activation, classical pathway signal transduction response to unfolded protein interspecies interaction between organisms regulatory region DNA binding immunoglobulin mediated immune response cell surface receptor linked signaling pathway cellular response to ionizing radiation positive regulation vascular endothelial growth factor production protein targeting to membrane acute-phase response extracellular region gastrulation activation of caspase activity purinergic nucleotide receptor activity, G-protein coupled purine nucleotide biosynthetic process release of cytochrome c from mitochondria negative regulation of phosphorylation cysteine-type peptidase activity regulation of immune response regulation of cyclin-dependent protein kinase activity cellular response to mechanical stimulus cysteine-type endopeptidase activity antigen binding aging cell communication chromosome response to organic substance signal transducer activity induction of apoptosis by extracellular signals response to bacterium Table S2. continued