Table S4. List of genes significantly changed in late acute phase vs convalescent phase (HG-focus platform) Probeset IDGene SymbolGene Titlep-valueFold-Change _atIFI27interferon, alpha-inducible protein _s_atRRM2ribonucleotide reductase M24.66E _atTYMSthymidylate synthetase8.37E _atTNFRSF17 tumor necrosis factor receptor superfamily, member E _s_atCD38CD38 molecule2.24E _s_atZWINTZW10 interactor1.70E _atNUSAP1nucleolar and spindle associated protein 11.33E _s_atCDKN3cyclin-dependent kinase inhibitor 32.47E _atBUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)2.91E _s_atGMNNgeminin, DNA replication inhibitor5.05E _s_atCDC20cell division cycle 20 homolog (S. cerevisiae)3.34E _s_atFABP5fatty acid binding protein 5 (psoriasis-associated)1.77E _s_atCKS2CDC28 protein kinase regulatory subunit 26.20E _atGGH gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)2.65E _atCCNA2cyclin A23.63E _atCCNB2cyclin B21.48E _s_atAPOBEC3B apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B1.74E _atPCNAproliferating cell nuclear antigen1.00E _x_atPTTG1pituitary tumor-transforming 11.78E _atCDK1cyclin-dependent kinase 13.50E _atTOP2Atopoisomerase (DNA) II alpha 170kDa4.16E _atPBKPDZ binding kinase4.33E _atKIF11kinesin family member E _s_atBIRC5baculoviral IAP repeat-containing 56.14E _s_atNCAPGnon-SMC condensin I complex, subunit G5.81E _s_atTPX2 TPX2, microtubule-associated, homolog (Xenopus laevis)1.81E _atIGJ immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptid2.28E _s_atFKBP11FK506 binding protein 11, 19 kDa6.97E _atUAP1UDP-N-acteylglucosamine pyrophosphorylase 12.45E _atMCM6minichromosome maintenance complex component 61.37E _s_atGINS2GINS complex subunit 2 (Psf2 homolog)6.75E _atELL2elongation factor, RNA polymerase II, 21.62E _s_atMAD2L1MAD2 mitotic arrest deficient-like 1 (yeast)4.59E _atNDC80 NDC80 homolog, kinetochore complex component (S. cerevisiae)9.55E _s_atRACGAP1Rac GTPase activating protein 11.52E _atUBE2Cubiquitin-conjugating enzyme E2C8.74E _s_atHMMRhyaluronan-mediated motility receptor (RHAMM)5.76E _atXBP1X-box binding protein 11.57E _s_atAURKAaurora kinase A1.33E _s_atCENPAcentromere protein A1.39E _atIFI44Linterferon-induced protein 44-like5.48E _s_atEZH2enhancer of zeste homolog 2 (Drosophila)1.09E _s_atFEN1flap structure-specific endonuclease 18.11E _s_atPRC1protein regulator of cytokinesis 11.45E _atRFC4replication factor C (activator 1) 4, 37kDa5.64E _atPRDX4peroxiredoxin 44.57E _s_atHSP90B1heat shock protein 90kDa beta (Grp94), member 16.61E _atBUB1B budding uninhibited by benzimidazoles 1 homolog beta (yeast)4.14E _atMAN1A1mannosidase, alpha, class 1A, member 11.79E

Table S4 continued _s_atSAR1BSAR1 homolog B (S. cerevisiae)1.91E _s_atMCM2minichromosome maintenance complex component 21.31E _atGZMB granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)1.93E _atTTKTTK protein kinase2.86E _s_atSLAMF7SLAM family member 74.92E _s_atISG15ISG15 ubiquitin-like modifier1.56E _atMANFmesencephalic astrocyte-derived neurotrophic factor6.68E _atSERPING1serpin peptidase inhibitor, clade G (C1 inhibitor), member 11.87E _s_atITM2Cintegral membrane protein 2C6.02E _atMX1 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)8.38E _s_atSTMN1stathmin 17.58E _s_atCHEK1CHK1 checkpoint homolog (S. pombe)2.55E _atPOU2AF1POU class 2 associating factor 11.45E _s_atSDF2L1stromal cell-derived factor 2-like 14.24E _atGBP1guanylate binding protein 1, interferon-inducible, 67kDa1.34E _atKIF15kinesin family member E _atCCNA2cyclin A29.68E _s_atPPIBpeptidylprolyl isomerase B (cyclophilin B)3.18E _s_atSLC1A4 solute carrier family 1 (glutamate/neutral amino acid transporter), member 41.15E _atSMC4structural maintenance of chromosomes 41.82E _atIFIT1interferon-induced protein with tetratricopeptide repeats 19.89E _s_atSUB1SUB1 homolog (S. cerevisiae)1.66E _atTK1thymidine kinase 1, soluble1.94E _s_atRRM1ribonucleotide reductase M15.73E _atHIST1H4Chistone cluster 1, H4c1.14E _atPOLE2polymerase (DNA directed), epsilon 2 (p59 subunit)5.24E _atUSP18ubiquitin specific peptidase E _atHIST1H1Chistone cluster 1, H1c2.86E _s_atFBXO5F-box protein 56.76E _atTRIP13thyroid hormone receptor interactor E _s_atMKI67antigen identified by monoclonal antibody Ki E _s_atIDH2isocitrate dehydrogenase 2 (NADP+), mitochondrial4.82E _atCASP3caspase 3, apoptosis-related cysteine peptidase7.13E _atAURKBaurora kinase B6.41E _atNME1non-metastatic cells 1, protein (NM23A) expressed in5.37E _s_atCDC45cell division cycle 45 homolog (S. cerevisiae)9.65E _s_atCKS1BCDC28 protein kinase regulatory subunit 1B6.18E _atDUSP5dual specificity phosphatase 52.65E _s_atIFI44interferon-induced protein E _s_at AKAP2 /// PALM2- AKAP2A kinase (PRKA) anchor protein 2 /// PALM2-AKAP2 readthrough1.05E _s_atLAP3leucine aminopeptidase 35.62E _atKIF20Akinesin family member 20A5.81E _s_atAURKAaurora kinase A2.05E _atKIF4Akinesin family member 4A6.91E _atCENPEcentromere protein E, 312kDa2.56E _s_atCDC6cell division cycle 6 homolog (S. cerevisiae)9.43E _atIFI6interferon, alpha-inducible protein 65.04E _atMYL6Bmyosin, light chain 6B, alkali, smooth muscle and non-muscle2.57E _s_atMCM5minichromosome maintenance complex component 55.53E _atSRP54signal recognition particle 54kDa9.43E _s_atACOT7acyl-CoA thioesterase 71.22E _s_atCTNNAL1catenin (cadherin-associated protein), alpha-like 15.55E _atTUBG1tubulin, gamma 16.68E _atISG20interferon stimulated exonuclease gene 20kDa4.65E _atSLC35B1solute carrier family 35, member B12.40E _atKPNA2karyopherin alpha 2 (RAG cohort 1, importin alpha 1)8.63E _s_atPDIA5protein disulfide isomerase family A, member 56.07E

Table S4 continued _atMTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate c1.35E _s_atUBE2Subiquitin-conjugating enzyme E2S6.79E _atCCR2chemokine (C-C motif) receptor 27.05E _s_atPAICS phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxami2.24E _x_atHIST1H2BHhistone cluster 1, H2bh8.15E _s_atRBBP8retinoblastoma binding protein 85.57E _s_atTPD52tumor protein D523.08E _atPDIA4protein disulfide isomerase family A, member 47.73E _atRAD51AP1RAD51 associated protein 12.36E _atTGFBItransforming growth factor, beta-induced, 68kDa1.88E _atPPP1R15Aprotein phosphatase 1, regulatory (inhibitor) subunit 15A1.33E _atTCL1AT-cell leukemia/lymphoma 1A2.78E _s_atTNFtumor necrosis factor5.43E _atIL13RA1interleukin 13 receptor, alpha 12.25E _atTREM1triggering receptor expressed on myeloid cells 11.51E _atCD1CCD1c molecule8.66E _atCD83CD83 molecule4.04E _atCLEC4AC-type lectin domain family 4, member A1.36E _s_at CCL3 /// CCL3L1 /// CCL3L3 chemokine (C-C motif) ligand 3 /// chemokine (C-C motif) ligand 3-like 1 /// chemokine8.76E _s_atCPVLcarboxypeptidase, vitellogenic-like3.65E _atNELL2NEL-like 2 (chicken)3.76E _s_atIER3immediate early response 31.18E _x_atMS4A1membrane-spanning 4-domains, subfamily A, member 16.95E _s_atG0S2G0/G1switch 27.36E _atLGALS2lectin, galactoside-binding, soluble, 23.02E _atIL1Binterleukin 1, beta9.15E _s_atCACNA2D3calcium channel, voltage-dependent, alpha 2/delta subunit 31.37E _atCDKN1Ccyclin-dependent kinase inhibitor 1C (p57, Kip2)2.34E _atRTN1reticulon 16.96E _atPTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)2.79E _x_atHBA1 /// HBA2hemoglobin, alpha 1 /// hemoglobin, alpha 23.00E _s_atIL8interleukin 89.14E _x_atHBA1 /// HBA2hemoglobin, alpha 1 /// hemoglobin, alpha 21.87E _x_atHBBhemoglobin, beta3.24E