functionEnrichment

ScoreEnrichment p-

value% genes in group that are present

# genes in list, in group

type I interferon-mediated signaling pathway 48.1918 1.18E-21 33.3333 21cytokine-mediated signaling pathway 44.7086 3.83E-20 18.4932 27response to virus 27.706 9.28E-13 16.3636 18immune response 22.0887 2.55E-10 8.48057 24innate immune response 18.0716 1.42E-08 8.7156 19interferon-gamma-mediated signaling pathway 18.0352 1.47E-08 17.4603 11double-stranded RNA binding 14.7506 3.93E-07 25.9259 7chemotaxis 13.1787 1.89E-06 11 11negative regulation of type I interferon production 10.6409 2.39E-05 25 5defense response to virus 10.5916 2.51E-05 18.1818 6inflammatory response 10.0085 4.50E-05 6.80628 13ISG15-protein conjugation 9.7455 5.86E-05 60 3phagocytosis, engulfment 9.7455 5.86E-05 60 3blood circulation 9.60189 6.76E-05 15.3846 6negative regulation of viral genome replication 9.27546 9.37E-05 28.5714 4response to biotic stimulus 9.06589 0.000115541 50 3positive regulation of interferon-alpha production 9.06589 0.000115541 50 3nucleosome 8.65279 0.000174639 13.0435 6IgG binding 8.5198 0.00019948 42.8571 3cellular copper ion homeostasis 8.06331 0.000314883 37.5 3superoxide-generating NADPH oxidase activity 7.67135 0.00046599 33.3333 3cell-cell signaling 7.65048 0.000475818 5.6872 12cellular response to heat 7.02319 0.00089098 27.2727 3copper ion transport 7.02319 0.00089098 27.2727 3nucleosome assembly 7.01185 0.000901144 9.67742 6ISG15 ligase activity 6.92111 0.000986732 66.6667 2regulation of defense response to virus 6.92111 0.000986732 66.6667 2intracellular transport of viral proteins in host cell 6.92111 0.000986732 66.6667 2cellular response to interferon-alpha 6.92111 0.000986732 66.6667 2interleukin-1 beta secretion 6.92111 0.000986732 66.6667 2detection of virus 6.92111 0.000986732 66.6667 2RNA catabolic process 6.50007 0.00150334 23.0769 3cytosol 6.27649 0.00187999 2.80496 43modification-dependent protein catabolic process 6.24007 0.00194972 50 2negative regulation of defense response to virus by host 6.24007 0.00194972 50 2pathogen-associated molecular pattern dependent induction by symbiont of host innate immunity 6.24007 0.00194972 50 2tryptophan catabolic process to kynurenine 6.24007 0.00194972 50 2protein kinase inhibitor activity 6.06264 0.00232824 20 3microglial cell activation involved in immune response 5.74133 0.0032105 40 2response to lipopolysaccharide 5.48064 0.00416668 6.30631 7negative regulation of erythrocyte differentiation 5.34793 0.00475797 33.3333 2tryptophan catabolic process 5.34793 0.00475797 33.3333 2hydrolase activity, acting on acid anhydrides 5.34793 0.00475797 33.3333 2positive regulation of immune response 5.02351 0.00658137 28.5714 2chemokine activity 4.87244 0.00765464 9.30233 4response to cold 4.81069 0.00814225 13.0435 3positive regulation of tumor necrosis factor biosynthetic process 4.74786 0.0086702 25 2JAK-STAT cascade 4.69049 0.00918223 12.5 3protein dimerization activity 4.59814 0.0100705 6.94444 5defense response to bacterium 4.56034 0.0104585 8.51064 4

Table S2. GO categories upregulated in early acute phase vs convalescent phase(P < 0.05) (HG-focus platform)

cyclin-dependent protein kinase inhibitor activity 4.50856 0.0110143 22.2222 2

soluble fraction 4.48521 0.0112745 3.73563 13

activation of pro-apoptotic gene products 4.36218 0.0127506 11.1111 3

positive regulation of interferon-beta production 4.29742 0.0136036 20 2

phosphatidylinositol binding 4.26213 0.0140923 10.7143 3

complement activation, classical pathway 4.26213 0.0140923 10.7143 3

signal transduction 4.18404 0.0152369 2.83533 26

response to unfolded protein 4.16619 0.0155112 10.3448 3

interspecies interaction between organisms 4.16437 0.0155395 4.03226 10

regulatory region DNA binding 4.10873 0.0164287 18.1818 2

immunoglobulin mediated immune response 4.10873 0.0164287 18.1818 2

cell surface receptor linked signaling pathway 3.94168 0.0194156 4.69799 7

cellular response to ionizing radiation 3.93837 0.01948 16.6667 2

positive regulation vascular endothelial growth factor production 3.93837 0.01948 16.6667 2

protein targeting to membrane 3.93837 0.01948 16.6667 2

acute-phase response 3.81825 0.0219662 9.09091 3

extracellular region 3.81514 0.0220346 2.65018 30

gastrulation 3.78326 0.0227485 15.3846 2

activation of caspase activity 3.68242 0.0251621 6.55738 4

purinergic nucleotide receptor activity, G-protein coupled 3.64103 0.0262252 14.2857 2

purine nucleotide biosynthetic process 3.50984 0.0299017 13.3333 2

release of cytochrome c from mitochondria 3.3882 0.0337695 12.5 2

negative regulation of phosphorylation 3.3882 0.0337695 12.5 2

cysteine-type peptidase activity 3.31663 0.0362749 7.5 3

regulation of immune response 3.28865 0.0373043 5.7971 4

regulation of cyclin-dependent protein kinase activity 3.19276 0.0410584 7.14286 3

cellular response to mechanical stimulus 3.19276 0.0410584 7.14286 3

cysteine-type endopeptidase activity 3.19276 0.0410584 7.14286 3

antigen binding 3.16898 0.0420466 11.1111 2

aging 3.14129 0.043227 4.7619 5

cell communication 3.13353 0.0435637 6.97674 3

chromosome 3.08169 0.0458817 4.22535 6

response to organic substance 3.07599 0.0461438 6.81818 3

signal transducer activity 3.07333 0.0462666 2.94118 15

induction of apoptosis by extracellular signals 3.0718 0.0463376 5.40541 4

response to bacterium 3.06959 0.0464404 10.5263 2

Table S2. continued