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 cycle E cell division E spindle organization E mitosis E cell cycle E DNA replication E M phase of mitotic cell cycle E chromosome E phosphatidylinositol-mediated signaling E cell cycle checkpoint E mitotic prometaphase E G1/S transition of mitotic cell cycle E DNA strand elongation involved in DNA replication E regulation of transcription involved in G1/S phase of mitotic cell cycle E spindle E nucleoplasm E cytosol E spindle microtubule E anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process E S phase of mitotic cell cycle E mitotic sister chromatid segregation E ATP binding E mitotic cell cycle spindle assembly checkpoint E spindle pole E regulation of cyclin-dependent protein kinase activity E condensed chromosome kinetochore E cytoskeleton E nucleotide binding E DNA-dependent DNA replication initiation E mitotic cell cycle checkpoint E microtubule-based movement E kinetochore E activation of anaphase-promoting complex activity E MCM complex E protein localization to kinetochore E anaphase-promoting complex E mitotic spindle organization E nucleus E type I interferon-mediated signaling pathway E M/G1 transition of mitotic cell cycle E midbody E microtubule motor activity E nucleobase-containing compound interconversion E protein binding E positive regulation of cell cycle cytokinesis E cytokinesis E mitotic chromosome condensation telomere maintenance via semi-conservative replication cytokine-mediated signaling pathway cell proliferation telomere maintenance via recombination regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle microtubule

Table S5 continued DNA repair glycerol ether metabolic process G2/M transition of mitotic cell cycle chromosome, centromeric region chromosome segregation kinetochore assembly condensed nuclear chromosome, centromeric region condensin complex spindle midzone assembly involved in mitosis condensed chromosome outer kinetochore condensed chromosome, centromeric region response to virus negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle perinuclear region of cytoplasm positive regulation of exit from mitosis mitotic metaphase cytoplasm protein disulfide oxidoreductase activity nucleoside-triphosphatase activity telomere maintenance nucleotide-excision repair, DNA gap filling DNA replication checkpoint endoplasmic reticulum lumen mitotic cell cycle G2/M transition DNA damage checkpoint establishment of mitotic spindle orientation DNA replication factor C complex melanosome centrosome protein disulfide isomerase activity gamma-tubulin binding spindle midzone DNA metabolic process cell redox homeostasis positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle positive regulation of viral genome replication tubulin binding chromosome organization magnesium ion binding exonuclease activity nucleotide biosynthetic process mitotic metaphase/anaphase transition oocyte maturation positive regulation of DNA binding protein serine/threonine kinase activity nucleolus protein peptidyl-prolyl isomerization single-stranded DNA binding transcription-coupled nucleotide-excision repair isomerase activity microtubule binding microtubule cytoskeleton GTP binding cofactor binding negative regulation of DNA replication histone deacetylase binding protein K11-linked ubiquitination

protein K11-linked ubiquitination cysteine-type endopeptidase inhibitor activity organ regeneration nucleosome pyrimidine base metabolic process response to cadmium ion centriole positive regulation of mitotic cell cycle nuclear chromosome response to drug condensed nuclear chromosome protein kinase binding kinase activity reciprocal meiotic recombination nucleotide-excision repair protein N-linked glycosylation via asparagine peptidyl-prolyl cis-trans isomerase activity base-excision repair Table S5 continued