1. Table S5. GO categories upregulated in late acute vs convalescent phase(p <0.05) (HG-focus platform) functionEnrichment ScoreEnrichment p-value % genes in group that are present # genes in list, in group mitotic cell cycle60.65964.53E-2715.94233 cell division50.51671.15E-2217.93126 spindle organization33.73042.24E-15759 mitosis32.93694.96E-1517.894717 cell cycle30.89653.82E-149.8290623 DNA replication27.51591.12E-1214.414416 M phase of mitotic cell cycle27.18931.56E-122412 chromosome26.09464.65E-1211.971817 phosphatidylinositol-mediated signaling25.50558.38E-1221.052612 cell cycle checkpoint23.2188.25E-1113.461514 mitotic prometaphase22.72971.34E-1023.809510 G1/S transition of mitotic cell cycle21.84193.27E-1012.173914 DNA strand elongation involved in DNA replication21.38165.18E-1033.33338 regulation of transcription involved in G1/S phase of mitotic cell cycle20.5761.16E-0941.17657 spindle18.99565.63E-0916.666710 nucleoplasm18.95625.85E-094.3041630 cytosol18.94735.91E-093.0658847 spindle microtubule18.10861.37E-0830.43487 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process18.0341.47E-0815.151510 S phase of mitotic cell cycle17.52562.45E-0812.359611 mitotic sister chromatid segregation15.55611.75E-0745.45455 ATP binding14.77013.85E-073.4949331 mitotic cell cycle spindle assembly checkpoint14.64354.37E-0726.0876 spindle pole14.3345.95E-0718.42117 regulation of cyclin-dependent protein kinase activity13.61871.22E-0616.66677 condensed chromosome kinetochore13.38141.54E-0621.42866 cytoskeleton13.14061.96E-064.6341519 nucleotide binding13.07552.10E-063.0017235 DNA-dependent DNA replication initiation13.02592.20E-0629.41185 mitotic cell cycle checkpoint11.99946.15E-06404 microtubule-based movement11.82627.31E-0616.66676 kinetochore11.66038.63E-0616.21626 activation of anaphase-promoting complex activity11.57339.41E-06753 MCM complex11.57339.41E-06753 protein localization to kinetochore11.57339.41E-06753 anaphase-promoting complex11.55799.56E-0636.36364 mitotic spindle organization11.16281.42E-0533.33334 nucleus11.15631.43E-052.1284160 type I interferon-mediated signaling pathway10.83071.98E-0511.11117 M/G1 transition of mitotic cell cycle10.5222.69E-0510.60617 midbody10.23963.57E-0512.7666 microtubule motor activity9.863755.20E-0516.1295 nucleobase-containing compound interconversion9.64466.48E-0523.52944 protein binding9.612626.69E-052.0471959 positive regulation of cell cycle cytokinesis9.433868.00E-0542.85713 cytokinesis9.259239.52E-0514.28575 mitotic chromosome condensation8.973720.00012669637.53 telomere maintenance via semi-conservative replication8.964960.000127811204 cytokine-mediated signaling pathway8.82840.0001465126.164389 cell proliferation8.809260.0001493444.7244112 telomere maintenance via recombination8.764040.00015625219.04764 regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle8.749470.0001585469.836076 microtubule8.390850.0002269346.557388

2. Table S5 continued DNA repair8.293410.0002501595.2083310 glycerol ether metabolic process8.231280.000266195303 G2/M transition of mitotic cell cycle8.228630.0002669028.955226 chromosome, centromeric region7.606740.00049709114.28574 chromosome segregation7.606740.00049709114.28574 kinetochore assembly7.534640.00053425366.66672 condensed nuclear chromosome, centromeric region7.534640.00053425366.66672 condensin complex7.534640.00053425366.66672 spindle midzone assembly involved in mitosis7.534640.00053425366.66672 condensed chromosome outer kinetochore7.534640.00053425366.66672 condensed chromosome, centromeric region7.534640.00053425366.66672 response to virus7.297810.0006770186.363647 negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle7.101380.0008239679.090915 perinuclear region of cytoplasm7.040050.0008760854.1353411 positive regulation of exit from mitosis6.850350.00105909502 mitotic metaphase6.850350.00105909502 cytoplasm6.794390.001120041.8970256 protein disulfide oxidoreductase activity6.749810.001171118.753 nucleoside-triphosphatase activity6.740250.0011823511.42864 telomere maintenance6.632810.0013164611.11114 nucleotide-excision repair, DNA gap filling6.565460.0014081717.64713 DNA replication checkpoint6.348360.00174962402 endoplasmic reticulum lumen6.014310.002443547.142865 mitotic cell cycle G2/M transition DNA damage checkpoint5.951720.0026013533.33332 establishment of mitotic spindle orientation5.951720.0026013533.33332 DNA replication factor C complex5.951720.0026013533.33332 melanosome5.890560.002765446.944445 centrosome5.817620.002974684.929587 protein disulfide isomerase activity5.624080.003609928.57142 gamma-tubulin binding5.624080.003609928.57142 spindle midzone5.345210.00477097252 DNA metabolic process5.31230.0049305711.53853 cell redox homeostasis5.001220.0067297410.34483 positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle4.945920.007112387.017544 positive regulation of viral genome replication4.888350.00753387202 tubulin binding4.696460.0091275318.18182 chromosome organization4.696460.0091275318.18182 magnesium ion binding4.670120.00937115.208335 exonuclease activity4.522920.010857316.66672 nucleotide biosynthetic process4.522920.010857316.66672 mitotic metaphase/anaphase transition4.522920.010857316.66672 oocyte maturation4.522920.010857316.66672 positive regulation of DNA binding4.522920.010857316.66672 protein serine/threonine kinase activity4.260120.01412063.389838 nucleolus4.248990.01427872.4390216 protein peptidyl-prolyl isomerization4.219230.014709914.28572 single-stranded DNA binding4.181520.01527527.692313 transcription-coupled nucleotide-excision repair4.113230.01635487.53 isomerase activity4.095740.01664355.479454 microtubule binding4.046910.01747637.317073 microtubule cytoskeleton4.046910.01747637.317073 GTP binding4.034350.01769723.517597 cofactor binding3.960090.019061412.52 negative regulation of DNA replication3.960090.019061412.52 histone deacetylase binding3.919790.01984536.976743 protein K11-linked ubiquitination3.843650.021415211.76472

3. protein K11-linked ubiquitination3.843650.021415211.76472 cysteine-type endopeptidase inhibitor activity3.843650.021415211.76472 organ regeneration3.799460.02238296.666673 nucleosome3.741650.0237156.521743 pyrimidine base metabolic process3.734590.023882911.11112 response to cadmium ion3.734590.023882911.11112 centriole3.632080.026461210.52632 positive regulation of mitotic cell cycle3.632080.026461210.52632 nuclear chromosome3.535420.0291466102 response to drug3.522290.02953172.952038 condensed nuclear chromosome3.444020.03193599.523812 protein kinase binding3.370750.03436393.731345 kinase activity3.210920.04031943.571435 reciprocal meiotic recombination3.196750.0408958.333332 nucleotide-excision repair3.190930.04113385.263163 protein N-linked glycosylation via asparagine3.062980.046748353 peptidyl-prolyl cis-trans isomerase activity3.050620.04732957.692312 base-excision repair3.050620.04732957.692312 Table S5 continued